FAIL bioperl-1.4 i386-freebsd-thread-multi 6.1-release-p6

This distribution has been tested as part of the cpan-testers
effort to test as many new uploads to CPAN as possible.  See
http://testers.cpan.org/

Please cc any replies to cpan-testers@perl.org to keep other
test volunteers informed and to prevent any duplicate effort.

--

Dear Ewan Birney,
    
This is a computer-generated error report created automatically by
CPANPLUS, version 0.82. Testers personal comments may appear 
at the end of this report.


Thank you for uploading your work to CPAN.  However, it appears that
there were some problems testing your distribution.

TEST RESULTS:

Below is the error stack from stage 'make test':

[MSG] [Thu Aug 23 14:46:06 2007] Trying to get 'ftp://ftp.cpan.org/pub/CPAN/authors/id/L/LI/LIMAONE/Bio-Grep-v0.10.0.tar.gz'
[MSG] [Thu Aug 23 14:46:07 2007] Trying to get 'ftp://ftp.cpan.org/pub/CPAN/authors/id/L/LI/LIMAONE/CHECKSUMS'
[MSG] [Thu Aug 23 14:46:07 2007] Checksum matches for 'Bio-Grep-v0.10.0.tar.gz'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/README'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/TODO'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/lib/'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Backend/'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Backend/Vmatch.pm'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Backend/RE.pm'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Backend/GUUGle.pm'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Backend/Agrep.pm'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Backend/BackendI.pm'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Benchmarks.pod'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Cookbook.pod'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Root.pm'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Filter/'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Filter/FilterI.pm'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Filter/FilterRemoveDuplicates.pm'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/SearchSettings.pm'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/SearchResult.pm'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep.pm'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/META.yml'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/Makefile.PL'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/script/'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/script/bgrep'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/script/benchmark.pl'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/Build.PL'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/pod-coverage.t'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/Test.fasta'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/Test_pep.fasta'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/pod.t'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/TestFilter.pm'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/00.checkprereq.t'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/00.load.t'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/50.synopsis.t'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/perlcritic.t'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/Test2.fasta'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/11.backends.guugle.t'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/40.utils.t'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/Test_query_revcom.fasta'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/11.backends.re.t'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/BioGrepTest.pm'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/10.backends.all.t'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/30.features.alignments.t'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/TestGUUGleExtend.fasta'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/20.filter.t'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/BioGrepSkip.pm'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/TestRevCom.fasta'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/t/Test_query.fasta'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/Changes'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio-Grep-v0.10.0/MANIFEST'
[MSG] [Thu Aug 23 14:46:07 2007] Extracted 'Bio::Grep' to '/home/plu/blead/.cpanplus/5.9.5/build/Bio-Grep-v0.10.0'
[MSG] [Thu Aug 23 14:46:07 2007] Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Root::Version 0 not found.
Warning: prerequisite Carp::Assert 0 not found.
Warning: prerequisite Class::MethodMaker 2.02 not found.
Warning: prerequisite IO::String 1 not found.
Warning: prerequisite ToolSet 0.13 not found.
Warning: prerequisite UNIVERSAL::require 0.11 not found.
Writing Makefile for Bio::Grep

[MSG] [Thu Aug 23 14:46:07 2007] DEFAULT 'filter_prereqs' HANDLER RETURNING 'sub return value'
[MSG] [Thu Aug 23 14:46:07 2007] Module 'Bio::Grep' requires 'Bio::Root::Version' version '0' to be installed 
[MSG] [Thu Aug 23 14:46:07 2007] Module 'Bio::Grep' requires 'Carp::Assert' version '0' to be installed 
[MSG] [Thu Aug 23 14:46:07 2007] Module 'Bio::Grep' requires 'Class::MethodMaker' version '2.02' to be installed 
[MSG] [Thu Aug 23 14:46:08 2007] Module 'Bio::Grep' requires 'IO::String' version '1' to be installed 
[MSG] [Thu Aug 23 14:46:08 2007] Module 'Bio::Grep' requires 'ToolSet' version '0.13' to be installed 
[MSG] [Thu Aug 23 14:46:08 2007] Module 'Bio::Grep' requires 'UNIVERSAL::require' version '0.11' to be installed 
[MSG] [Thu Aug 23 14:46:08 2007] Trying to get 'ftp://ftp.cpan.org/pub/CPAN/authors/id/B/BI/BIRNEY/bioperl-1.4.tar.gz'
[MSG] [Thu Aug 23 14:46:09 2007] Trying to get 'ftp://ftp.cpan.org/pub/CPAN/authors/id/B/BI/BIRNEY/CHECKSUMS'
[MSG] [Thu Aug 23 14:46:09 2007] Checksum matches for 'bioperl-1.4.tar.gz'
[MSG] [Thu Aug 23 14:46:12 2007] Extracted 'bioperl-1.4/'
[MSG] [Thu Aug 23 14:46:12 2007] Extracted 'bioperl-1.4/DEPRECATED'
[MSG] [Thu Aug 23 14:46:12 2007] Extracted 'bioperl-1.4/AUTHORS'
[MSG] [Thu Aug 23 14:46:12 2007] Extracted 'bioperl-1.4/BUGS'
[MSG] [Thu Aug 23 14:46:12 2007] Extracted 'bioperl-1.4/Changes'
[MSG] [Thu Aug 23 14:46:12 2007] Extracted 'bioperl-1.4/INSTALL'
[MSG] [Thu Aug 23 14:46:12 2007] Extracted 'bioperl-1.4/FAQ'
[MSG] [Thu Aug 23 14:46:12 2007] Extracted 'bioperl-1.4/Bio/'
[MSG] [Thu Aug 23 14:46:12 2007] Extracted 'bioperl-1.4/Bio/Align/'
[MSG] [Thu Aug 23 14:46:12 2007] Extracted 'bioperl-1.4/Bio/Align/AlignI.pm'
[MSG] [Thu Aug 23 14:46:12 2007] Extracted 'bioperl-1.4/Bio/Align/DNAStatistics.pm'
[MSG] [Thu Aug 23 14:46:12 2007] Extracted 'bioperl-1.4/Bio/Align/PairwiseStatistics.pm'
[MSG] [Thu Aug 23 14:46:12 2007] Extracted 'bioperl-1.4/Bio/Align/StatisticsI.pm'
[MSG] [Thu Aug 23 14:46:12 2007] Extracted 'bioperl-1.4/Bio/Align/Utilities.pm'
[MSG] [Thu Aug 23 14:46:12 2007] Extracted 'bioperl-1.4/Bio/AlignIO.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AnalysisI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AnalysisParserI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AnalysisResultI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AnnotatableI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AnnotationCollectionI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AnnotationI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/ClusterI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/ClusterIO.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DBLinkContainerI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DasI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DescribableI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/FeatureHolderI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/IdCollectionI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/IdentifiableI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/LocatableSeq.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/LocationI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/MapIO.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/OntologyIO.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Perl.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/PrimarySeq.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/PrimarySeqI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Range.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/RangeI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/SearchDist.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/SearchIO.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Seq.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/SeqAnalysisParserI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/SeqFeatureI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/SeqI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/SeqIO.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/SeqUtils.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/SimpleAlign.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/SimpleAnalysisI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Species.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Taxonomy.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/TreeIO.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/UpdateableSeqI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/WebAgent.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AlignIO/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AlignIO/bl2seq.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AlignIO/clustalw.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AlignIO/emboss.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AlignIO/fasta.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AlignIO/maf.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AlignIO/mase.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AlignIO/mega.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AlignIO/meme.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AlignIO/metafasta.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AlignIO/msf.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AlignIO/nexus.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AlignIO/pfam.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AlignIO/phylip.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AlignIO/prodom.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AlignIO/psi.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AlignIO/selex.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/AlignIO/stockholm.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Annotation/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Annotation/AnnotationFactory.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Annotation/Collection.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Annotation/Comment.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Annotation/DBLink.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Annotation/OntologyTerm.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Annotation/Reference.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Annotation/SimpleValue.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Annotation/StructuredValue.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Annotation/TypeManager.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Assembly/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Assembly/IO/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Assembly/IO/phrap.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Assembly/IO/ace.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Assembly/Contig.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Assembly/ContigAnalysis.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Assembly/IO.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Assembly/Scaffold.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Assembly/ScaffoldI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/IO/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/IO/medline2ref.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/IO/medlinexml.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/IO/pubmed2ref.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/IO/pubmedxml.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/Article.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/BiblioBase.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/Book.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/BookArticle.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/IO.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/Journal.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/JournalArticle.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/MedlineArticle.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/MedlineBook.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/MedlineBookArticle.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/MedlineJournal.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/MedlineJournalArticle.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/Organisation.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/Patent.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/Person.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/Proceeding.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/Provider.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/PubmedArticle.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/PubmedBookArticle.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/PubmedJournalArticle.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/Ref.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/Service.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/TechReport.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/Thesis.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Biblio/WebResource.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Cluster/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Cluster/ClusterFactory.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Cluster/FamilyI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Cluster/SequenceFamily.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Cluster/UniGene.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Cluster/UniGeneI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/ClusterIO/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/ClusterIO/dbsnp.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/ClusterIO/unigene.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/CodonUsage/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/CodonUsage/Table.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/CodonUsage/IO.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Coordinate/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Result/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Result/Match.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Result/Gap.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Chain.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Collection.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Coordinate/ExtrapolatingPair.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Coordinate/GeneMapper.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Graph.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Coordinate/MapperI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Pair.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Result.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Coordinate/ResultI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Utils.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/BiblioI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Ace.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Biblio/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Biblio/biofetch.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Biblio/soap.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/BioFetch.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/CUTG.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/DBFetch.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/EMBL.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Failover.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Fasta.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/FileCache.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Flat.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GDB.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GenBank.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GenPept.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/InMemoryCache.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/MANIFEST'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Makefile.PL'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/MeSH.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/NCBIHelper.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/QueryI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/RandomAccessI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/RefSeq.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Registry.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/SeqI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/SwissProt.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Taxonomy.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Universal.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/UpdateableSeqI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/WebDBSeqI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/XEMBL.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/XEMBLService.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/fasta.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/embl.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/genbank.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/swiss.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/swissprot.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BinarySearch.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/biofetch.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/ace.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/iterator.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/mysql.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/oracle.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/oracleace.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/pg.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/biofetch_oracle.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/memory.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/memory_iterator.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Featname.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Feature.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Homol.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/RelSegment.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Segment.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Typename.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/alignment.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/clone.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/coding.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/match.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/none.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/processed_transcript.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/transcript.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_acembly.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_genscan.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_refgene.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_softberry.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_unigene.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Util/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Util/Binning.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Util/Rearrange.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Query/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Query/GenBank.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Query/WebQuery.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Taxonomy/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Taxonomy/entrez.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/DB/Taxonomy/flatfile.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Das/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Das/FeatureTypeI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Das/SegmentI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Event/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Event/EventGeneratorI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Event/EventHandlerI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Expression/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Expression/FeatureGroup/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Expression/FeatureGroup.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Expression/FeatureI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Expression/FeatureSet/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Expression/FeatureSet/FeatureSetMas50.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Factory/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Factory/AnalysisI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Factory/ApplicationFactoryI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Factory/DriverFactory.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Factory/FTLocationFactory.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Factory/HitFactoryI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Factory/LocationFactoryI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Factory/MapFactoryI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Factory/ObjectBuilderI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Factory/ObjectFactory.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Factory/ObjectFactoryI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Factory/ResultFactoryI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Factory/SeqAnalysisParserFactory.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Factory/SeqAnalysisParserFactoryI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Factory/SequenceFactoryI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Factory/SequenceProcessorI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Factory/SequenceStreamI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Factory/TreeFactoryI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/FeatureFile/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/FeatureFile/Iterator.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/ConfiguratorI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Feature.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/FeatureFile.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Panel.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Pictogram.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/RendererI.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Util.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/Factory.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/alignment.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/anchored_arrow.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/arrow.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/box.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/cds.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/crossbox.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/diamond.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/dna.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/dot.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/ellipse.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/ex.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/extending_arrow.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/generic.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/graded_segments.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/group.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/heterogeneous_segments.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/line.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/minmax.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/oval.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/pinsertion.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/primers.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/processed_transcript.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/redgreen_box.pm'
[MSG] [Thu Aug 23 14:46:13 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/redgreen_segment.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/rndrect.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/ruler_arrow.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/segmented_keyglyph.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/segments.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/span.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/splice_site.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/toomany.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/track.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/transcript.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/transcript2.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/translation.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/triangle.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/xyplot.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Index/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Index/Abstract.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Index/AbstractSeq.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Index/Blast.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Index/EMBL.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Index/Fasta.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Index/Fastq.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Index/GenBank.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Index/SwissPfam.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Index/Swissprot.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/BioPerl.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/Loader.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/README'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/SRS.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/AARange.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Chain.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/ChainI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/DNA.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Exon.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Gene.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Intron.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Mutation.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Mutator.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Prim_Transcript.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Range.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Repeat_Region.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Repeat_Unit.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/SeqI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Transcript.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Translation.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Location/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Location/Atomic.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Location/AvWithinCoordPolicy.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Location/CoordinatePolicyI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Location/Fuzzy.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Location/FuzzyLocationI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Location/NarrowestCoordPolicy.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Location/Simple.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Location/Split.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Location/SplitLocationI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Location/WidestCoordPolicy.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Map/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Map/CytoMap.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Map/CytoMarker.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Map/CytoPosition.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Map/LinkageMap.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Map/LinkagePosition.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Map/MapI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Map/MappableI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Map/Marker.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Map/MarkerI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Map/Microsatellite.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Map/OrderedPosition.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Map/OrderedPositionWithDistance.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Map/Position.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Map/PositionI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Map/SimpleMap.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/MapIO/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/MapIO/mapmaker.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/IO/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/IO/phylip.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/IO/scoring.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/PsmHeader.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/Psm.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/InstanceSite.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/InstanceSiteI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/transfac.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/mast.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/meme.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/PsmHeaderI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/PsmI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/SiteMatrix.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/SiteMatrixI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/Generic.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/IO.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/MatrixI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/PhylipDist.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Matrix/Scoring.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/GOterm.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/InterProTerm.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/Ontology.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/OntologyEngineI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/OntologyI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/OntologyStore.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/Path.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/PathI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/Relationship.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/RelationshipFactory.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/RelationshipI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/RelationshipType.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/SimpleGOEngine.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/SimpleOntologyEngine.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/Term.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/TermFactory.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/TermI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/BaseSAXHandler.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/InterProHandler.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/InterProParser.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/dagflat.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/goflat.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/simplehierarchy.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/soflat.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/MeSH/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/MeSH/Term.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/MeSH/Twig.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/MiniMIMentry.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/OMIMentry.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/OMIMparser.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/Correlate.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/Measure.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/Phenotype.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/PhenotypeI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/IO/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/IO/csv.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/IO/prettybase.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/Genotype.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/GenotypeI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/IO.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/Individual.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/IndividualI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/Marker.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/MarkerI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/PopStats.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/Population.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/PopulationI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/Statistics.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/Simulation/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/Simulation/Coalescent.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/Simulation/GeneticDrift.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Restriction/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme/MultiCut.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme/MultiSite.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Restriction/Analysis.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Restriction/EnzymeCollection.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Restriction/EnzymeI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Restriction/IO.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Restriction/IO/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Restriction/IO/bairoch.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Restriction/IO/base.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Restriction/IO/itype2.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Restriction/IO/withrefm.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Root/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Root/Exception.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Root/Err.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Root/Global.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Root/HTTPget.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Root/IO.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Root/IOManager.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Root/Object.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Root/Root.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Root/RootI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Root/Storable.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Root/Utilities.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Root/Vector.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Root/Version.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Root/Xref.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/BlastHSP.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/FastaHSP.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/GenericHSP.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/HMMERHSP.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/HSPFactory.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/HSPI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/PSLHSP.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/PsiBlastHSP.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/WABAHSP.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/BlastHit.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/Fasta.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/GenericHit.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/HMMERHit.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/HitFactory.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/HitI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/PsiBlastHit.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/BlastUtils.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/DatabaseI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/GenericDatabase.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Processor.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/SearchUtils.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Iteration/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Iteration/GenericIteration.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Iteration/IterationI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Result/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Result/BlastResult.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Result/GenericResult.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Result/HMMERResult.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Result/ResultFactory.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Result/ResultI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Search/Result/WABAResult.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/BSMLResultWriter.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/GbrowseGFF.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/HSPTableWriter.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/HTMLResultWriter.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/HitTableWriter.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/ResultTableWriter.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/TextResultWriter.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/EventHandlerI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/FastHitEventBuilder.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/IteratedSearchResultEventBuilder.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/SearchResultEventBuilder.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/SearchWriterI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/axt.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/blast.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/blasttable.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/blastxml.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/exonerate.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/fasta.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/hmmer.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/megablast.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/psl.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/sim4.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/waba.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SearchIO/wise.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/Meta/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/Meta/Array.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/BaseSeqProcessor.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/EncodedSeq.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/LargePrimarySeq.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/LargeSeq.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/Meta.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/MetaI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/PrimaryQual.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/PrimedSeq.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/QualI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/RichSeq.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/RichSeqI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/SeqBuilder.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/SeqFactory.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/SeqFastaSpeedFactory.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/SeqWithQuality.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/SequenceTrace.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/Seq/TraceI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/ExonI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Exon.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/GeneStructure.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/GeneStructureI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Intron.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/NC_Feature.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Poly_A_site.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Promoter.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Transcript.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/TranscriptI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/UTR.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/AnnotationAdaptor.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Collection.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/CollectionI.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Computation.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/FeaturePair.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Generic.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/PositionProxy.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Primer.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Similarity.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/SimilarityPair.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/SiRNA/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/SiRNA/Oligo.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/SiRNA/Pair.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Tools/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Tools/TypeMapper.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Tools/Unflattener.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game/'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game/featHandler.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game/gameHandler.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game/gameSubs.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game/gameWriter.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game/seqHandler.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/FTHelper.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/MultiFile.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/abi.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/ace.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/alf.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/asciitree.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/bsml.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/chadoxml.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/ctf.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/embl.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/exp.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/fasta.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/fastq.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/gcg.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/genbank.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/kegg.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/largefasta.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/locuslink.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/metafasta.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/phd.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/pir.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/pln.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/qual.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/raw.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/scf.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/swiss.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/tab.pm'
[MSG] [Thu Aug 23 14:46:14 2007] Extracted 'bioperl-1.4/Bio/SeqIO/tigr.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/SeqIO/ztr.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Structure/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Structure/Chain.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Structure/Atom.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Structure/IO/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Structure/IO/pdb.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Structure/Entry.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Structure/IO.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Structure/Model.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Structure/Residue.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Structure/StructureI.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Structure/SecStr/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Structure/SecStr/DSSP/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Structure/SecStr/DSSP/Res.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Structure/SecStr/STRIDE/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Structure/SecStr/STRIDE/Res.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Symbol/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Symbol/Alphabet.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Symbol/AlphabetI.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Symbol/DNAAlphabet.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Symbol/ProteinAlphabet.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Symbol/README.Symbol'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Symbol/Symbol.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Symbol/SymbolI.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Taxonomy/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Taxonomy/FactoryI.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Taxonomy/Node.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Taxonomy/Taxon.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Taxonomy/Tree.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Alignment/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Alignment/Consed.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Alignment/Trim.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/AlignFactory.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/AnalysisResult.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/BPbl2seq.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/BPlite.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/BPpsilite.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Blat.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/CodonTable.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Coil.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/ECnumber.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/EPCR.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/ESTScan.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Eponine.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Est2Genome.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/FootPrinter.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/GFF.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Gel.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Geneid.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Genemark.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Genewise.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Genomewise.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Genscan.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Glimmer.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Grail.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/GuessSeqFormat.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Hmmpfam.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/IUPAC.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Lucy.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/MZEF.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/OddCodes.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer3.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Prints.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Profile.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Promoterwise.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/PrositeScan.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Pseudowise.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/QRNA.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/RandomDistFunctions.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/RepeatMasker.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/RestrictionEnzyme.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Seg.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/SeqAnal.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/SeqPattern.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/SeqStats.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/SeqWords.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/SiRNA.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Sigcleave.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Signalp.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Tmhmm.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/WWW.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/dpAlign.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/pICalculator.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/pSW.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/DNA/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/DNA/ESEfinder.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/SimpleAnalysisBase.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Domcut.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/ELM.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/GOR4.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/HNN.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Mitoprot.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/NetPhos.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Scansite.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Sopma.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/BPlite/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/BPlite/Iteration.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/BPlite/HSP.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/BPlite/Sbjct.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast/Sbjct.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast/CHANGES'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast/HSP.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast/HTML.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast/README'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/EMBOSS/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/EMBOSS/Palindrome.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/HMMER/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/HMMER/Domain.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/HMMER/Results.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/HMMER/Set.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Molphy/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Molphy/Result.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Molphy.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML/ModelResult.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML/Result.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Phylip/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Phylip/ProtDist.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Prediction/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Prediction/Exon.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Prediction/Gene.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer/Assessor/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer/Assessor/Base.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer/AssessorI.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer/Feature.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer/Pair.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Run/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Run/README'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Run/RemoteBlast.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Run/StandAloneBlast.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Run/WrapperBase.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Sim4/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Sim4/Results.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tools/Sim4/Exon.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tree/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tree/AlleleNode.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tree/Node.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tree/NodeI.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tree/NodeNHX.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tree/RandomFactory.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tree/Statistics.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tree/Tree.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tree/TreeFunctionsI.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Tree/TreeI.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/TreeIO/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/TreeIO/TreeEventBuilder.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/TreeIO/lintree.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/TreeIO/newick.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/TreeIO/nexus.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/TreeIO/nhx.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/TreeIO/svggraph.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/TreeIO/tabtree.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Variation/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Variation/IO/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Variation/IO/flat.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Variation/IO/xml.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Variation/AAChange.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Variation/AAReverseMutate.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Variation/Allele.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Variation/DNAMutation.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Variation/IO.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Variation/README'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Variation/RNAChange.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Variation/SNP.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Variation/SeqDiff.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Bio/Variation/VariantI.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/faq/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/faq/faq.html'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/faq/faq.dtd'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/faq/faq.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/faq/faq.xml'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/makedoc.PL'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/examples/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/blastn.out'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/data1.txt'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/embl2picture.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/factor7.embl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast1.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast2.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast3.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast4.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_features.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/examples/README'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/figs/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig1.png'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig2.png'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig3.png'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig4.png'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig5.png'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig6.png'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/figs/README'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/html/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/html/images/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/html/images/tip.png'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/html/Flat_Databases.html'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/html/Graphics-HOWTO.html'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/html/OBDA_Access.html'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/html/PAML.html'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/html/README'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/html/SearchIO.html'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/html/SeqIO.html'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/html/SimpleWebAnalysis.html'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/html/e-novative.css'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/pdf/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/pdf/Flat_Databases.pdf'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/pdf/Graphics-HOWTO.pdf'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/pdf/OBDA_Access.pdf'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/pdf/PAML.pdf'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/pdf/SearchIO.pdf'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/pdf/SeqIO.pdf'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/pdf/SimpleWebAnalysis.pdf'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/pdf/Trees.pdf'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/sgml/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/sgml/Feature-Annotation.sgml'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/sgml/Flat_Databases.sgml'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/sgml/Graphics-HOWTO.sgml'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/sgml/OBDA_Access.sgml'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/sgml/PAML.sgml'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/sgml/README'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/sgml/SearchIO.sgml'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/sgml/SeqIO.sgml'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/sgml/SimpleWebAnalysis.sgml'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/sgml/Trees.sgml'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/txt/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/txt/Flat_Databases.txt'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/doc/howto/txt/SimpleWebAnalysis.txt'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/INSTALL.WIN'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/LICENSE'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/MANIFEST.SKIP'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/Makefile.PL'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/PLATFORMS'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/README'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/biodatabases.pod'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/biodesign.pod'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/bioperl.lisp'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/bioperl.pod'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/bioscripts.pod'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/bptutorial.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/Bio-DB-GFF/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/Bio-DB-GFF/load_ucsc.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/bioperl.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/generate_random_seq.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/longorf.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/make_mrna_protein.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/make_primers.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/rev_and_trans.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/revcom_dir.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/subsequence.cgi'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/align/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/align/align_on_codons.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/align/aligntutorial.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/align/clustalw.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/align/simplealign.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/biblio/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/biblio/biblio_examples.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/biblio/biblio_soap.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/biographics/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/biographics/all_glyphs.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/biographics/dynamic_glyphs.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/biographics/feature_data.gff'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/biographics/feature_data.txt'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/biographics/lots_of_glyphs.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/biographics/render_sequence.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/cluster/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/cluster/dbsnp.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/contributed/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/contributed/nmrpdb_parse.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/contributed/prosite2perl.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/contributed/rebase2list.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/db/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/db/get_seqs.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/db/dbfetch'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/db/est_tissue_query.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/db/gb2features.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/db/getGenBank.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/db/rfetch.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/db/use_registry.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/liveseq/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/liveseq/change_gene.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/popgen/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/popgen/parse_calc_stats.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/root/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/root/lib/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/root/lib/Bio/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/root/lib/Bio/PrimarySeq.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/root/lib/Bio/PrimarySeqI.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/root/lib/Bio/Seq.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/root/lib/Bio/SeqI.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/root/lib/Error.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/root/lib/TestInterface.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/root/lib/TestObject.pm'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/root/README'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/root/exceptions1.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/root/exceptions2.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/root/exceptions3.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/root/exceptions4.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/searchio/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/searchio/blast_example.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/searchio/custom_writer.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/searchio/hitwriter.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/searchio/hspwriter.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/searchio/htmlwriter.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/searchio/psiblast_features.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/searchio/psiblast_iterations.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/searchio/rawwriter.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/searchio/resultwriter.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/searchio/waba2gff.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/sirna/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/sirna/TAG'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/sirna/rnai_finder.cgi'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/tk/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/tk/gsequence.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/tk/hitdisplay.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/tools/'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/tools/gb_to_gff.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/tools/gff2ps.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/tools/parse_codeml.pl'
[MSG] [Thu Aug 23 14:46:15 2007] Extracted 'bioperl-1.4/examples/tools/psw.pl'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/examples/tools/restriction.pl'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/examples/tools/run_genscan.pl'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/examples/tools/seq_pattern.pl'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/examples/tools/standaloneblast.pl'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/examples/tree/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/examples/tree/paup2phylip.pl'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/maintenance/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/maintenance/authors.pl'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/maintenance/README'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/maintenance/modules.pl'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/maintenance/pod.pl'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/models/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/models/biblio.dia'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/models/README'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/models/bio_liveseq_variation.dia'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/models/bio_map.dia'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/models/bio_restriction.dia'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/models/bioperl.dia'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/models/coordinatemapper.dia'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/models/map_proposal.txt'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/models/maps_and_markers.dia'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/models/popgen.dia'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/models/population_proposal.txt'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/load_gff.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/README'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/TAG'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/bp_genbank2gff.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/bulk_load_gff.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/fast_load_gff.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/generate_histogram.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/load_ucsc.pl'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/pg_bulk_load_gff.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_gadfly.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_ncbi_human.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_sgd.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_wormbase.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/install_bioperl_scripts.pl'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/DB/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/DB/TAG'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/DB/biofetch_genbank_proxy.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/DB/bioflat_index.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/DB/biogetseq.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/DB/flanks.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/biblio/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/biblio/TAG'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/biblio/biblio.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/das/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/das/README'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/das/TAG'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/graphics/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/graphics/frend.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/graphics/README'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/graphics/TAG'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/graphics/feature_draw.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/graphics/search_overview.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/index/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/index/TAG'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/index/bp_fetch.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/index/bp_index.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/popgen/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/popgen/composite_LD.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/popgen/heterogeneity_test.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/searchio/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/searchio/filter_search.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/seq/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/seq/TAG'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/seq/extract_feature_seq.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/seq/seqconvert.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/seq/split_seq.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/seq/translate_seq.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/seqstats/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/seqstats/TAG'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/seqstats/aacomp.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/seqstats/chaos_plot.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/seqstats/gccalc.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/seqstats/oligo_count.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/taxa/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/taxa/TAG'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/taxa/local_taxonomydb_query.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/taxa/taxid4species.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/tree/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/tree/TAG'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/tree/blast2tree.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/utilities/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/utilities/bp_nrdb.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/utilities/README'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/utilities/TAG'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/utilities/bp_mrtrans.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/utilities/bp_sreformat.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/utilities/dbsplit.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/utilities/mask_by_search.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/utilities/mutate.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/utilities/pairwise_kaks.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/utilities/remote_blast.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/utilities/search2BSML.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/utilities/search2alnblocks.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/utilities/search2gff.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/utilities/search2tribe.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/scripts/utilities/seq_length.PLS'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/biodbgff/'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/biodbgff/test.gff'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/503384.MEGABLAST.0'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/503384.MEGABLAST.2'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/5X_1895.FASTXY'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/AAC12660.fa'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/AB077698.gb'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/AE003528_ecoli.bls'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/AE003644_Adh-genomic.gb'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/AF032047.gbk'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/AF165282.gb'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/AHCYL1.kegg'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/ATF14F8.gbk'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/AY095303S1.gbk'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/AnnIX-v003.gbk'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/BK000016-tpa.gbk'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/BLOSUM50'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/BN000066-tpa.embl'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/D10483.gbk'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/D12555.gbk'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/ECAPAH02.embl'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/GO.defs.test'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/GO.defs.test2'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/Genscan.FastA'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.FASTA'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.fa'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.gff'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.grail'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.grailexp'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.mzef'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.tblastx'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/L77119.hmmer'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/LL-sample.seq'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/LOAD_Ccd1.dnd'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/LittleChrY.dbsnp.xml'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/MmCT'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/NM_002254.gb'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/NT_021877.gbk'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/PAM250'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/SwissProt.dat'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/U58726.gb'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/X98338_Adh-mRNA.gb'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/a_thaliana.blastn'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/aaml.mlc'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/aaml_pairwise.mlc'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/acefile.ace.1'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/acefile.singlets'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/alnfile.fasta'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/amino.fa'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/ar.embl'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/bl2seq.blastn'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/bl2seq.blastn.rev'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/bl2seq.blastx.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/bl2seq.bug940.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/bl2seq.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/bl2seq.tblastx.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/blast.report'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/blat.psLayout3'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/c200-vs-yeast.BLASTN'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/c200-vs-yeast.BLASTN.m8'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/chad100.scf'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/codeml.mlc'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/codeml_nssites.mlc'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/compLD_missingtest.prettybase'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/compLD_test.prettybase'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/component.ontology.test'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/component.ontology.test2'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/crab.dat.cn'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/crab.nj'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/crab.njb'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/crypto.sim4-0'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/crypto.sim4-3'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/crypto.sim4-4'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/cys1_dicdi.water'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/cysprot.fa'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/cysprot.msf'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/cysprot.needle'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/cysprot.tblastn'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/cysprot.water'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/cysprot1.FASTA'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/cysprot1.fa'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/cysprot1a.fa'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/cysprot1a.msf'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/cysprot1b.fa'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/cysprot1b.hmmsearch'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/cysprot1b.msf'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/cysprot1b.newick'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/cysprot_vs_gadfly.FASTA'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/dmel_2Lchunk.gb'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/dna1.fa'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/dna2.fa'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/dnaE-bsub-prot.fa'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/dnaE-bsub.fa'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/dnaEbsub_ecoli.wublastx'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/dnaEbsub_ecoli.wutblastn'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/dnaEbsub_ecoli.wutblastx'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/ecoli-trna-qrna.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/ecoli_domains.rps.xml'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/ecoli_domains.rpsblast'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/ecolitst.bls'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/ecolitst.fa'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/ecolitst.wublastp'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/empty.bl2seq'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/expected.blast.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/factor7.embl'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/footprinter.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/geneid_1.0.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/genemark.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/genewise.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/genewise_output.paracel_btk'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/genomewise.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/genomic-seq.epcr'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/genomic-seq.fasta'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/genomic-seq.genscan'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/genomic-seq.mzef'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/gf-s71.needle'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/glimmer.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/hemoglobinA.meg'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/hg16_chroms.gff'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/hmmpfam.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/hmmsearch.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/hs_est.est2genome'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/hs_fugu.newick'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/hs_owlmonkey.fas'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/hs_owlmonkey.fasta'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/hsinsulin.blastcl3.blastn'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/humor.maf'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/humts1.pal'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/insulin.water'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/interpro_short.xml'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/lucy.info'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/lucy.qual'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/lucy.seq'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/lucy.stderr'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/lysozyme6.protml'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/lysozyme6.simple.protml'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/mapmaker.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/mast.dat'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/megablast_output.paracel_btk'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/meme.dat'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/mpath.ontology.test'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/multi_1.fa'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/multi_2.fa'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/multi_blast.bls'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/multifa.seq'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/multiseq.bls'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/mus.bls.xml'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/mutations.dat'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/mutations.xml'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/myco_sites.gff'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/nei_gojobori_test.aln'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/neighbor.dist'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/no-genes.genscan'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/no_hsps.blastp'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/noninterleaved.phy'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/omim_genemap_test'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/omim_text_test'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/pdb1bpt.ent'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/phi.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/phipsi.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/phredfile.phd'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/phylipdist-36.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/phylipdist.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/pictogram.fa'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/plague_yeast.bls.xml'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/polymorphism.dat'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/polymorphism.xml'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/popgen_saureus.dat'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/popgen_saureus.multidat'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/popstats.prettybase'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/roa1.dat'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/primedseq.fa'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/primer3_infile.txt'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/primer3_outfile.txt'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/primer3_output.txt'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/promoterwise.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/protpars.phy'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/psiblastreport.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/qrna-relloc.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/qualfile.qual'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/rebase.itype2'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/rebase.withrefm'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/repeatmasker.fa.out'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/revcomp_mrna.gb'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/roa1.genbank'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/roa1.swiss'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/sbay_c545-yeast.BLASTZ.PSL'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/seqdatabase.ini'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/seqfile.pir'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/seqs.fas'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/sequencefamily.dat'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/short.blx'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/sim4.for.for'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/sim4.for.rev'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/sim4.rev'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/sofa.ontology'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/sparsealn.needle'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/stress_test_medline.xml'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/stress_test_pubmed.xml'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/swiss.dat'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/swisspfam.data'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.ace'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.embl'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.fasta'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.game'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.gcg'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.gcgblast'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.gcgfasta'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.genbank'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.genbank.noseq'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.mase'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.metafasta'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.nh'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.nhx'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.pfam'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.pir'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.raw'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.swiss'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.tab'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.txt'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test.waba'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/test_badlf.gcg'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/testaln.aln'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/testaln.fasta'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/testaln.mase'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/testaln.metafasta'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/testaln.msf'
[MSG] [Thu Aug 23 14:46:16 2007] Extracted 'bioperl-1.4/t/data/testaln.nexus'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/testaln.pfam'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/testaln.phylip'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/testaln.prodom'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/testaln.selex'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/testaln.stockholm'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/testdat.exonerate'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/testdbaccnums.out'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/testfuzzy.genbank'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/transfac.dat'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/unigene.data'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/version2.scf'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/version3.scf'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/worm_fam_2785.cdna'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/yn00.mlc'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version1.gif'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version1.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version2.gif'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version2.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version3.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version4.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version5.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version6.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version7.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version8.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version1.gif'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version1.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version10.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version11.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version12.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version13.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version14.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version2.gif'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version2.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version3.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version4.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version5.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version6.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version7.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version8.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version9.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/feature_data.txt'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version1.gif'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version1.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version2.gif'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version2.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version3.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version4.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version5.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version6.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version7.png'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.contigs'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.log'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.ace.1'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs.qual'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.log'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.problems'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.problems.qual'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.qual'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.singlets'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.view'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.newtags'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.phrap.out'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.screen.out'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_projectNewChromats.fof'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project_to_alu.cross'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4922R.phd.1'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4924F.phd.1'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4924R.phd.1'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4947F.phd.1'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/dbfa/'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/dbfa/1.fa'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/dbfa/2.fa'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/dbfa/3.fa'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/dbfa/4.fa'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/dbfa/5.fa'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/dbfa/6.fa'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/dbfa/7.fa'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/registry/'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/registry/bdb/'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/registry/bdb/seqdatabase.ini'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/registry/flat/'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/data/registry/flat/seqdatabase.ini'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/AAChange.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/AAReverseMutate.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/AlignIO.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/AlignStats.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Allele.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Alphabet.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Annotation.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/AnnotationAdaptor.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Assembly.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/BPbl2seq.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/BPlite.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/BPpsilite.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Biblio.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/BiblioReferences.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Biblio_biofetch.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/BioDBGFF.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/BioFetch_DB.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/BioGraphics.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/BlastIndex.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Chain.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/ClusterIO.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Coalescent.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/CodonTable.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/CoordinateGraph.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/CoordinateMapper.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Correlate.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/CytoMap.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/DB.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/DBCUTG.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/DBFasta.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/DNAMutation.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Domcut.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/ECnumber.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/ELM.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/EMBL_DB.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/EMBOSS_Tools.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/ESEfinder.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/EncodedSeq.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Exception.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Exonerate.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/FootPrinter.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/GDB.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/GFF.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/GOR4.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/GOterm.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/GeneCoordinateMapper.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Geneid.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Genewise.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Genomewise.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Genpred.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/GuessSeqFormat.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/HNN.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/IUPAC.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Index.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/InstanceSite.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/InterProParser.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/LinkageMap.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/LiveSeq.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/LocatableSeq.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Location.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/LocationFactory.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/LocusLink.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Map.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/MapIO.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Matrix.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/MeSH.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Measure.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/MetaSeq.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/MicrosatelliteMarker.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/MiniMIMentry.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/MitoProt.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Molphy.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Mutation.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Mutator.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/NetPhos.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Node.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/OMIMentry.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/OMIMentryAllelicVariant.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/OMIMparser.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/OddCodes.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Ontology.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/OntologyEngine.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/PAML.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Perl.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Phenotype.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/PhylipDist.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Pictogram.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/PopGen.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/PopGenSims.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/PrimarySeq.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Primer.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Promoterwise.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/ProtDist.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/QRNA.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/RNAChange.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/RandDistFunctions.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/RandomTreeFactory.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Range.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/RangeI.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/RefSeq.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Registry.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Relationship.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/RelationshipType.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/RemoteBlast.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/RepeatMasker.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/RestrictionAnalysis.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/RestrictionEnzyme.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/RestrictionIO.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/RootI.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/RootIO.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/RootStorable.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/SNP.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Scansite.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/SearchDist.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/SearchIO.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/Seq.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/SeqAnalysisParser.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/SeqBuilder.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/SeqDiff.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/SeqFeatCollection.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/SeqFeature.t'
[MSG] [Thu Aug 23 14:46:17 2007] Extracted 'bioperl-1.4/t/SeqIO.t'
[MSG] [Thu Aug 23 14:4