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Postings from September 2007
FAIL bioperl-1.4 i686-linux-thread-multi-64int 2.6.18-4-k7
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From:
andreas.koenig.gmwojprw
Date:
September 10, 2007 08:31
Subject:
FAIL bioperl-1.4 i686-linux-thread-multi-64int 2.6.18-4-k7
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 test report for bioperl-1.4, created
automatically by CPAN::Reporter, version 0.99_08, and sent to the CPAN
Testers mailing list. If you have received this email directly, it is
because the person testing your distribution chose to send a copy to your
CPAN email address; there may be a delay before the official report is
received and processed by CPAN Testers.
Thank you for uploading your work to CPAN. However, it appears that
there were some problems testing your distribution.
Sections of this report:
* Tester comments
* Prerequisites
* Environment and other context
* Test output
------------------------------
TESTER COMMENTS
------------------------------
Additional comments from tester:
[none provided]
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
-------------- ---- -----
DB_File 0 1.810
File::Spec 0 3.25
File::Temp 0 0.18
HTML::Entities 0 1.35
IO::Scalar 0 2.110
IO::String 0 1.08
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
LANG = C
PATH = /usr/lib/ccache:/home/sand/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/usr/local/perl/bin:/usr/X11/bin:/sbin:/usr/sbin
PERL5LIB =
PERL5_CPANPLUS_IS_RUNNING = 5258
PERL5_CPAN_IS_RUNNING = 5258
PERL_MM_USE_DEFAULT = 1
SHELL = /usr/bin/zsh
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
Perl: $^X = /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/bin/perl
UID: $< = 1005
EUID: $> = 1005
GID: $( = 1005 1005
EGID: $) = 1005 1005
Perl module toolchain versions installed:
Module Have
------------------- -------
CPAN 1.91_53
Cwd 3.25
ExtUtils::CBuilder 0.19
ExtUtils::Command 1.13
ExtUtils::Install 1.44
ExtUtils::MakeMaker 6.36
ExtUtils::Manifest 1.51
ExtUtils::ParseXS 2.18
File::Spec 3.25
Module::Build 0.2808
Module::Signature 0.55
Test::Harness 2.99_02
Test::More 0.70
YAML 0.65
YAML::Syck 0.97
version 0.7203
------------------------------
TEST OUTPUT
------------------------------
Output from '/usr/bin/make test':
PERL_DL_NONLAZY=1 /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/AAChange.....................ok
t/AAReverseMutate..............ok
t/AlignIO......................ok
t/AlignStats...................ok
t/Allele.......................ok
t/Alphabet.....................ok
t/Annotation...................ok
t/AnnotationAdaptor............ok
t/Assembly.....................ok
t/Biblio.......................SOAP::Lite not installed. Skipping some tests.
ok
t/Biblio_biofetch..............ok
t/BiblioReferences.............ok
t/BioDBGFF.....................ok
t/BioFetch_DB.................. Failed 1/27 subtests
t/BioGraphics..................GD or Text::Shellwords modules are not installed. This means that Bio::Graphics module is unusable. Skipping tests.
ok
t/BlastIndex...................ok
t/BPbl2seq.....................ok
t/BPlite.......................ok
t/BPpsilite....................ok
t/Chain........................ok
t/cigarstring..................ok
t/ClusterIO....................XML::Parser::PerlSAX not loaded. This means ClusterIO::dbsnp test cannot be executed. Skipping
ok
t/Coalescent...................ok
t/CodonTable...................ok
t/consed.......................ok
t/CoordinateGraph..............ok
t/CoordinateMapper.............ok
t/Correlate....................ok
t/CytoMap......................ok
t/DB...........................ok
t/DBCUTG.......................ok
t/DBFasta......................ok
t/DNAMutation..................ok
t/Domcut.......................ok
t/ECnumber.....................ok
t/ELM..........................
-------------------- WARNING ---------------------
MSG: Bio::Tools::Analysis::Protein::ELM Request Error:
400 URL must be absolute
Content-Type: text/plain
Client-Date: Mon, 10 Sep 2007 14:58:09 GMT
Client-Warning: Internal response
400 URL must be absolute
---------------------------------------------------
ok
t/EMBL_DB...................... Failed 3/15 subtests
t/EMBOSS_Tools.................ok
t/EncodedSeq...................ok
t/ePCR.........................ok
t/ESEfinder....................ok
t/est2genome...................ok
t/Exception....................ok
t/Exonerate....................ok
t/flat.........................ok
t/FootPrinter..................ok
t/game.........................XML::Parser::PerlSAX not loaded. This means game test cannot be executed. Skipping
ok
t/GDB..........................ok
t/GeneCoordinateMapper.........
-------------------- WARNING ---------------------
MSG: sorted sublocation array requested but root location doesn't define seq_id (at least one sublocation does!)
---------------------------------------------------
-------------------- WARNING ---------------------
MSG: sorted sublocation array requested but root location doesn't define seq_id (at least one sublocation does!)
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/Coordinate/GeneMapper.pm line 814.
ok
t/Geneid.......................ok
t/Genewise.....................ok
t/Genomewise...................ok
t/Genpred......................ok
t/GFF..........................Filehandle GEN0 opened only for output at /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/Root/IO.pm line 440.
Filehandle GEN1 opened only for output at /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/Root/IO.pm line 440.
ok
t/GOR4.........................ok
t/GOterm.......................ok
t/GuessSeqFormat...............Bio::SeqIO: game cannot be found
Exception
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::SeqIO::game. Can't locate XML/Parser/PerlSAX.pm in @INC (@INC contains: t .. /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/arch /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/lib/5.8.5/i686-linux-thread-multi-64int /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/lib/5.8.5 /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/lib/site_perl/5.8.5/i686-linux-thread-multi-64int /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/lib/site_perl/5.8.5 /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/lib/site_perl .) at /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/SeqIO/game/gameSubs.pm line 70.
BEGIN failed--compilation aborted at /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/SeqIO/game/gameSubs.pm line 70.
Compilation failed in require at /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/SeqIO/game/gameHandler.pm line 62.
BEGIN failed--compilation aborted at /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/SeqIO/game/gameHandler.pm line 62.
Compilation failed in require at /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/SeqIO/game.pm line 76.
BEGIN failed--compilation aborted at /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/SeqIO/game.pm line 76.
Compilation failed in require at /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/Root/Root.pm line 394.
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/Root/Root.pm:328
STACK: Bio::Root::Root::_load_module /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/Root/Root.pm:396
STACK: Bio::SeqIO::_load_format_module /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/SeqIO.pm:549
STACK: Bio::SeqIO::new /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/SeqIO.pm:377
STACK: t/GuessSeqFormat.t:61
-----------------------------------------------------------
For more information about the SeqIO system please see the SeqIO docs.
This includes ways of checking for formats at compile time, not run time
Failed 1/46 subtests
t/hmmer........................ok
t/HNN..........................ok
t/Index........................ok
t/InstanceSite.................ok
t/InterProParser...............Bio::OntologyIO: InterProParser cannot be found
Exception
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::OntologyIO::InterProParser. Can't locate XML/Parser/PerlSAX.pm in @INC (@INC contains: t .. . ./blib/lib /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/arch /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/lib/5.8.5/i686-linux-thread-multi-64int /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/lib/5.8.5 /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/lib/site_perl/5.8.5/i686-linux-thread-multi-64int /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/lib/site_perl/5.8.5 /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/lib/site_perl) at Bio/OntologyIO/InterProParser.pm line 84.
BEGIN failed--compilation aborted at Bio/OntologyIO/InterProParser.pm line 84.
Compilation failed in require at Bio/Root/Root.pm line 394.
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:328
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:396
STACK: Bio::OntologyIO::_load_format_module Bio/OntologyIO.pm:255
STACK: Bio::OntologyIO::new Bio/OntologyIO.pm:165
STACK: t/InterProParser.t:52
-----------------------------------------------------------
For more information about the OntologyIO system please see the docs.
This includes ways of checking for formats at compile time, not run time
Can't call method "next_ontology" on an undefined value at t/InterProParser.t line 59.
Dubious, test returned 2 (wstat 512, 0x200)
Failed 1/47 subtests
t/IUPAC........................ok
t/largefasta...................ok
t/largepseq....................ok
t/LinkageMap...................ok
t/LiveSeq......................ok
t/LocatableSeq.................ok
t/Location.....................ok
t/LocationFactory..............ok
t/LocusLink....................ok
t/lucy.........................ok
t/Map..........................ok
t/MapIO........................ok
t/Matrix.......................ok
t/Measure......................ok
t/MeSH.........................Use of uninitialized value in substitution (s///) at /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/DB/MeSH.pm line 263.
Use of uninitialized value in regexp compilation at /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/DB/MeSH.pm line 277.
Use of uninitialized value in regexp compilation at /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/DB/MeSH.pm line 277.
Use of uninitialized value in regexp compilation at /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/DB/MeSH.pm line 277.
Failed 1/26 subtests
t/MetaSeq......................ok
t/MicrosatelliteMarker.........ok
t/MiniMIMentry.................ok
t/MitoProt.....................ok
t/Molphy.......................ok
t/multiple_fasta...............ok
t/Mutation.....................ok
t/Mutator......................ok
t/NetPhos......................ok
t/Node.........................ok
t/OddCodes.....................ok
t/OMIMentry....................ok
t/OMIMentryAllelicVariant......ok
t/OMIMparser...................ok
t/Ontology.....................set_attribute: not a compat02 graph at /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/lib/site_perl/5.8.5/Graph.pm line 2394, <GEN0> line 10.
Dubious, test returned 9 (wstat 2304, 0x900)
Failed 50/50 subtests
t/OntologyEngine...............ok
t/PAML.........................ok
t/Perl.........................ok
t/phd..........................ok
t/Phenotype....................ok
t/PhylipDist...................ok
t/pICalculator.................ok
t/Pictogram....................ok
t/PopGen.......................ok
t/PopGenSims...................ok
t/primaryqual..................ok
t/PrimarySeq...................ok
t/primedseq....................ok
t/Primer.......................ok
t/primer3......................ok
t/Promoterwise.................ok
t/ProtDist.....................ok
t/psm..........................ok
t/QRNA.........................ok
t/qual.........................ok
t/RandDistFunctions............ok
t/RandomTreeFactory............ok
t/Range........................ok
t/RangeI.......................ok
t/RefSeq.......................ok
t/Registry.....................ok
t/Relationship.................ok
t/RelationshipType.............ok
t/RemoteBlast..................ok
t/RepeatMasker.................ok
t/RestrictionAnalysis..........ok
t/RestrictionEnzyme............ok
t/RestrictionIO................ok
t/RNAChange....................ok
t/RootI........................ok
t/RootIO.......................ok
t/RootStorable.................ok
t/Scansite.....................ok
t/scf..........................ok
t/SearchDist...................ok
t/SearchIO.....................XML::Parser::PerlSAX or HTML::Entities not loaded. This means SearchIO::blastxml test cannot be executed. Skipping
ok
t/Seq..........................ok
t/SeqAnalysisParser............ok
t/SeqBuilder...................ok
t/SeqDiff......................ok
t/SeqFeatCollection............ok
t/SeqFeature...................ok
t/seqfeaturePrimer.............ok
t/SeqIO........................ok
t/SeqPattern...................ok
t/SeqStats.....................ok
t/SequenceFamily...............ok
t/sequencetrace................ok
t/SeqUtils.....................ok
t/seqwithquality...............ok
t/SeqWords.....................ok
t/Sigcleave....................ok
t/Sim4.........................ok
t/SimilarityPair...............ok
t/SimpleAlign..................ok
t/simpleGOparser...............set_attribute: not a compat02 graph at /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/lib/site_perl/5.8.5/Graph.pm line 2394, <GEN1> line 14.
Dubious, test returned 9 (wstat 2304, 0x900)
Failed 98/98 subtests
t/sirna........................ok
t/SiteMatrix...................ok
t/SNP..........................ok
t/Sopma........................ok
t/Species......................ok
t/splicedseq...................ok
t/StandAloneBlast..............ok
t/StructIO.....................ok
t/Structure....................ok
t/Swiss........................ok
t/Symbol.......................ok
t/Taxonomy.....................ok
t/Tempfile.....................ok
t/Term.........................ok
t/Tools........................ok
t/Tree.........................ok
t/TreeIO.......................ok
t/trim.........................ok
t/tutorial.....................Bio::SeqIO: game cannot be found
Exception
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::SeqIO::game. Can't locate XML/Parser/PerlSAX.pm in @INC (@INC contains: . t /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/arch /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/lib/5.8.5/i686-linux-thread-multi-64int /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/lib/5.8.5 /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/lib/site_perl/5.8.5/i686-linux-thread-multi-64int /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/lib/site_perl/5.8.5 /home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390/lib/site_perl) at Bio/SeqIO/game/gameSubs.pm line 70.
BEGIN failed--compilation aborted at Bio/SeqIO/game/gameSubs.pm line 70.
Compilation failed in require at Bio/SeqIO/game/gameHandler.pm line 62.
BEGIN failed--compilation aborted at Bio/SeqIO/game/gameHandler.pm line 62.
Compilation failed in require at Bio/SeqIO/game.pm line 76.
BEGIN failed--compilation aborted at Bio/SeqIO/game.pm line 76.
Compilation failed in require at /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/Root/Root.pm line 394.
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/Root/Root.pm:328
STACK: Bio::Root::Root::_load_module /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/Root/Root.pm:396
STACK: Bio::SeqIO::_load_format_module /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/SeqIO.pm:549
STACK: Bio::SeqIO::new /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/Bio/SeqIO.pm:377
STACK: main::run_examples /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/bptutorial.pl:4027
STACK: t/tutorial.t:23
-----------------------------------------------------------
For more information about the SeqIO system please see the SeqIO docs.
This includes ways of checking for formats at compile time, not run time
Can't call method "next_seq" on an undefined value at /home/sand/.cpan/build/bioperl-1.4-HNXVm3/blib/lib/bptutorial.pl line 4035.
Dubious, test returned 2 (wstat 512, 0x200)
Failed 3/21 subtests
t/UCSCParsers..................ok
t/Unflattener..................ok
t/Unflattener2.................ok
t/UniGene......................ok
t/Variation_IO.................1d0
<
32d30
<
60d57
<
91d87
<
121d116
<
152d146
<
183d176
<
214d206
<
245d236
<
268d258
<
291d280
<
315d303
<
347d334
<
379d365
<
1d0
<
1,350c1,388
< ID M20132:(362)c.+4G>A; E2K
< Feature DNA; 1
< Feature /label: point, transition
< Feature /proof: computed
< Feature /location: 4
< Feature /upflank: gaagattcagccaagctcaaggatg
< Feature /change: g>a
< Feature /dnflank: aagtgcagttagggctgggaagggt
< Feature /re_site: -BccI
< Feature RNA; 1
< Feature /label: missense
< Feature /proof: experimental
< Feature /location: 4 (M20132::366)
< Feature /upflank: gaagattcagccaagctcaaggatg
< Feature /change: g>a
< Feature /dnflank: aagtgcagttagggctgggaagggt
< Feature /re_site: -BccI
< Feature /codon_table: 1
< Feature /codon: gaa>aaa; 1
< Feature /region: coding
< Feature AA; 1
< Feature /label: substitution, conservative
< Feature /proof: computed
< Feature /location: 2
< Feature /change: E>K
< //
< ID M20132:(362)c.+14T>A; L5X
< Feature DNA; 1
< Feature /label: point, transversion
< Feature /proof: computed
< Feature /location: 14
< Feature /upflank: ccaagctcaaggatggaagtgcagt
< Feature /change: t>a
< Feature /dnflank: agggctgggaagggtctaccctcgg
< Feature RNA; 1
< Feature /label: nonsense
< Feature /proof: experimental
< Feature /location: 14 (M20132::376)
< Feature /upflank: ccaagctcaaggatggaagtgcagt
< Feature /change: t>a
< Feature /dnflank: agggctgggaagggtctaccctcgg
< Feature /codon_table: 1
< Feature /codon: tta>taa; 2
< Feature /region: coding
< Feature AA; 1
< Feature /label: truncation
< Feature /proof: computed
< Feature /location: 5
< Feature /change: L>*
< //
< ID M20132:(362)c.+4G>A; E2K
< Feature DNA; 1
< Feature /label: point, transition
< Feature /proof: computed
< Feature /location: 4
< Feature /upflank: gaagattcagccaagctcaaggatg
< Feature /change: g>a
< Feature /dnflank: aagtgcagttagggctgggaagggt
< Feature /re_site: -BccI
< Feature RNA; 1
< Feature /label: missense
< Feature /proof: experimental
< Feature /location: 4 (M20132::366)
< Feature /upflank: gaagattcagccaagctcaaggatg
< Feature /change: g>a
< Feature /dnflank: aagtgcagttagggctgggaagggt
< Feature /re_site: -BccI
< Feature /codon_table: 1
< Feature /codon: gaa>aaa; 1
< Feature /region: coding
< Feature AA; 1
< Feature /label: substitution, conservative
< Feature /proof: computed
< Feature /location: 2
< Feature /change: E>K
< //
< ID M20132:(362)c.+100delATCCAG; I34del-2
< Feature DNA; 1
< Feature /label: deletion
< Feature /proof: computed
< Feature /location: 100..105
< Feature /upflank: tctgttccagagcgtgcgcgaagtg
< Feature /change: atccag>
< Feature /dnflank: aacccgggccccaggcacccagagg
< Feature /re_site: -BinI, -BsiYI, -DpnI, -Hpy178III, -MboI, +MjaIV
< Feature RNA; 1
< Feature /label: inframe, deletion
< Feature /proof: experimental
< Feature /location: 100..105 (M20132::462..467)
< Feature /upflank: tctgttccagagcgtgcgcgaagtg
< Feature /change: atccag>
< Feature /dnflank: aacccgggccccaggcacccagagg
< Feature /re_site: -BinI, -BsiYI, -DpnI, -Hpy178III, -MboI, +MjaIV
< Feature /codon_table: 1
< Feature /codon: atc>-; 1
< Feature /region: coding
< Feature AA; 1
< Feature /label: deletion
< Feature /proof: computed
< Feature /location: 34..35
< Feature /change: IQ>
< //
< ID M20132:(362)c.+101delT; I34delX172
< Feature DNA; 1
< Feature /label: deletion
< Feature /proof: computed
< Feature /location: 101
< Feature /upflank: ctgttccagagcgtgcgcgaagtga
< Feature /change: t>
< Feature /dnflank: ccagaacccgggccccaggcaccca
< Feature /re_site: -BinI, -DpnI, -Hpy178III, +MaeIII, -MboI, +Tsp45I
< Feature RNA; 1
< Feature /label: frameshift, deletion
< Feature /proof: experimental
< Feature /location: 101 (M20132::463)
< Feature /upflank: ctgttccagagcgtgcgcgaagtga
< Feature /change: t>
< Feature /dnflank: ccagaacccgggccccaggcaccca
< Feature /re_site: -BinI, -DpnI, -Hpy178III, +MaeIII, -MboI, +Tsp45I
< Feature /codon_table: 1
< Feature /codon: atc>-; 2
< Feature /region: coding
< Feature AA; 1
< Feature /label: out-of-frame translation, truncation
< Feature /proof: computed
< Feature /location: 34
< Feature /change: I>TRTRAPGTQRPRAQHLPAPVCCCCSSSSSSSSSSSSSSSSSSSSKRLAP
< Feature GSSSSSRVRMVLPKPIVEAPQATWSWMRNSNLHSRSRPWSATPREVASQSLEPPWPPAR
< Feature GCRSSCQHLRTRMTQLPHPRCPCWAPLSPA*
< //
< ID M20132:(362)c.+101insGGGCCC; I34ins+2
< Feature DNA; 1
< Feature /label: insertion
< Feature /proof: computed
< Feature /location: 100^101
< Feature /upflank: ctgttccagagcgtgcgcgaagtga
< Feature /change: >gggccc
< Feature /dnflank: tccagaacccgggccccaggcaccc
< Feature /re_site: +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI,
< Feature +DraII, +GsuI, +HaeIII, +HgiJII, -MboI, +MnlI, +NlaIV,
< Feature +SduI
< Feature RNA; 1
< Feature /label: inframe, insertion
< Feature /proof: experimental
< Feature /location: 100^101 (M20132::462^463)
< Feature /upflank: ctgttccagagcgtgcgcgaagtga
< Feature /change: >gggccc
< Feature /dnflank: tccagaacccgggccccaggcaccc
< Feature /re_site: +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI,
< Feature +DraII, +GsuI, +HaeIII, +HgiJII, -MboI, +MnlI, +NlaIV,
< Feature +SduI
< Feature /codon_table: 1
< Feature /codon: atc>-; 2
< Feature /region: coding
< Feature AA; 1
< Feature /label: insertion, complex
< Feature /proof: computed
< Feature /location: 34
< Feature /change: I>RAL
< //
< ID M20132:(362)c.+100insG; I34ins81X
< Feature DNA; 1
< Feature /label: insertion
< Feature /proof: computed
< Feature /location: 99^100
< Feature /upflank: tctgttccagagcgtgcgcgaagtg
< Feature /change: >g
< Feature /dnflank: atccagaacccgggccccaggcacc
< Feature /re_site: +BamHI, +BinI, +NlaIV, +XhoII
< Feature RNA; 1
< Feature /label: frameshift, insertion
< Feature /proof: experimental
< Feature /location: 99^100 (M20132::461^462)
< Feature /upflank: tctgttccagagcgtgcgcgaagtg
< Feature /change: >g
< Feature /dnflank: atccagaacccgggccccaggcacc
< Feature /re_site: +BamHI, +BinI, +NlaIV, +XhoII
< Feature /codon_table: 1
< Feature /codon: atc>-; 1
< Feature /region: coding
< Feature AA; 1
< Feature /label: out-of-frame translation, truncation
< Feature /proof: computed
< Feature /location: 34
< Feature /change: I>DPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*
< //
< ID M20132:(362)c.+100AT>GGGCCC; I34ins82X
< Feature DNA; 1
< Feature /label: complex
< Feature /proof: computed
< Feature /location: 100..101
< Feature /upflank: tctgttccagagcgtgcgcgaagtg
< Feature /change: at>gggccc
< Feature /dnflank: ccagaacccgggccccaggcaccca
< Feature /re_site: +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI,
< Feature +DraII, +HaeIII, +HgiJII, -Hpy178III, -MboI, +NlaIV, +SduI
< Feature RNA; 1
< Feature /label: frameshift, complex
< Feature /proof: experimental
< Feature /location: 100..101 (M20132::462..463)
< Feature /upflank: tctgttccagagcgtgcgcgaagtg
< Feature /change: at>gggccc
< Feature /dnflank: ccagaacccgggccccaggcaccca
< Feature /re_site: +ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI,
< Feature +DraII, +HaeIII, +HgiJII, -Hpy178III, -MboI, +NlaIV, +SduI
< Feature /codon_table: 1
< Feature /codon: atc>-; 1
< Feature /region: coding
< Feature AA; 1
< Feature /label: out-of-frame translation, truncation
< Feature /proof: computed
< Feature /location: 34
< Feature /change: I>GPPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*
< //
< ID M20132:(362+1)c.-1G>A
< Feature DNA; 1
< Feature /label: point, transition
< Feature /proof: computed
< Feature /location: -1
< Feature /upflank: ggtggaagattcagccaagctcaag
< Feature /change: g>a
< Feature /dnflank: atggaagtgcagttagggctgggaa
< Feature /re_site: -BccI, -FokI, +Hpy178III
< Feature RNA; 1
< Feature /label: unknown
< Feature /proof: experimental
< Feature /location: -1 (M20132::361)
< Feature /upflank: ggtggaagattcagccaagctcaag
< Feature /change: g>a
< Feature /dnflank: atggaagtgcagttagggctgggaa
< Feature /re_site: -BccI, -FokI, +Hpy178III
< Feature /region: 5'UTR
< //
< ID M20132:(362)c.+2766T>C
< Feature DNA; 1
< Feature /label: point, transition
< Feature /proof: computed
< Feature /location: 2766
< Feature /upflank: tctatttccacacccagtgaagcat
< Feature /change: t>c
< Feature /dnflank: ggaaaccctatttccccaccccagc
< Feature /re_site: +Hpy188I, +SfaNI, -XcmI
< Feature RNA; 1
< Feature /label: unknown
< Feature /proof: experimental
< Feature /location: 2766 (M20132::3128)
< Feature /upflank: tctatttccacacccagtgaagcat
< Feature /change: t>c
< Feature /dnflank: ggaaaccctatttccccaccccagc
< Feature /re_site: +Hpy188I, +SfaNI, -XcmI
< Feature /region: 3'UTR
< //
< ID J02933:(521)g.+12165A>G
< Feature DNA; 1
< Feature /label: point, transition
< Feature /proof: experimental
< Feature /location: 12165 (J02933::12686)
< Feature /upflank: cgcacacctgtggtgcctgccaccc
< Feature /change: a>g
< Feature /dnflank: ctgggttgcccatgattcatttttg
< Feature /re_site: +AciI, -BfiI, -BsrI, +FauI, +NspBII, +Sth132I,
< Feature -TspRI
< Feature /region: 3'UTR; (+1027)
< Feature RNA; 1
< Feature /label: unknown
< Feature /proof: computed
< Feature /location: 2428
< Feature /upflank: cgcacacctgtggtgcctgccaccc
< Feature /change: a>g
< Feature /dnflank: ctgggttgcccatgattcatttttg
< Feature /re_site: +AciI, -BfiI, -BsrI, +FauI, +NspBII, +Sth132I,
< Feature -TspRI
< Feature /region: 3'UTR; (-1)
< //
< ID J02933:(521)g.+4G>T; V2F
< Feature DNA; 1
< Feature /label: point, transversion
< Feature /proof: computed
< Feature /location: 4 (J02933::525)
< Feature /upflank: gcagcactgcagagatttcatcatg
< Feature /change: g>t
< Feature /dnflank: tctcccaggccctcaggctcctctg
< Feature /re_site: -BsmAI, -Eco31I
< Feature /region: exon; 1 (+4)
< Feature RNA; 1
< Feature /label: missense
< Feature /proof: experimental
< Feature /location: 4
< Feature /upflank: gcagcactgcagagatttcatcatg
< Feature /change: g>t
< Feature /dnflank: tctcccaggccctcaggctcctctg
< Feature /re_site: -BsmAI, -Eco31I
< Feature /codon_table: 1
< Feature /codon: gtc>ttc; 1
< Feature /region: coding
< Feature AA; 1
< Feature /label: substitution, nonconservative
< Feature /proof: computed
< Feature /location: 2
< Feature /change: V>F
< //
< ID J02933:(521)g.+1168G>T; D34Y
< Feature DNA; 1
< Feature /label: point, transversion
< Feature /proof: computed
< Feature /location: 1168 (J02933::1689)
< Feature /upflank: taaggcctcaggaggagaaacacgg
< Feature /change: g>t
< Feature /dnflank: acatgccgtggaagccggggcctca
< Feature /re_site: -BscGI, -Bsp24I, -CjePI, -FinI, +RsaI, -Sth132I,
< Feature +Tsp4CI
< Feature /region: exon; 1 (-29)
< Feature RNA; 1
< Feature /label: missense
< Feature /proof: experimental
< Feature /location: 100
< Feature /upflank: taaggcctcaggaggagaaacacgg
< Feature /change: g>t
< Feature /dnflank: acatgccgtggaagccggggcctca
< Feature /re_site: -BscGI, -Bsp24I, -CjePI, -FinI, +RsaI, -Sth132I,
< Feature +Tsp4CI
< Feature /codon_table: 1
< Feature /codon: gac>tac; 1
< Feature /region: coding
< Feature AA; 1
< Feature /label: substitution, nonconservative
< Feature /proof: computed
< Feature /location: 34
< Feature /change: D>Y
< //
< ID J02933:(521+1)g.-4C>G
< Feature DNA; 1
< Feature /label: point, transversion
< Feature /proof: computed
< Feature /location: -4 (J02933::518)
< Feature /upflank: ggcaggggcagcactgcagagattt
< Feature /change: c>g
< Feature /dnflank: atcatggtctcccaggccctcaggc
< Feature /re_site: +BclI, +DpnI, +MboI
< Feature /region: 5'UTR; (-4)
< Feature RNA; 1
< Feature /label: unknown
< Feature /proof: experimental
< Feature /location: -4
< Feature /upflank: ggcaggggcagcactgcagagattt
< Feature /change: c>g
< Feature /dnflank: atcatggtctcccaggccctcaggc
< Feature /re_site: +BclI, +DpnI, +MboI
< Feature /region: 5'UTR; (+31)
< //
---
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+4G>A" trivname="E2K">
> <DNA number="1" start="4" end="4" length="1" isMutation="1">
> <label>point</label>
> <label>transition</label>
> <proof>computed</proof>
> <upFlank>gaagattcagccaagctcaaggatg</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>a</allele_mut>
> <dnFlank>aagtgcagttagggctgggaagggt</dnFlank>
> <restriction_changes>-BccI</restriction_changes>
> </DNA>
> <RNA number="1" start="4" end="4" length="1" isMutation="1">
> <label>missense</label>
> <proof>experimental</proof>
> <upFlank>gaagattcagccaagctcaaggatg</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>a</allele_mut>
> <dnFlank>aagtgcagttagggctgggaagggt</dnFlank>
> <codon codon_ori="gaa" codon_mut="aaa" codon_pos="1"></codon>
> <restriction_changes>-BccI</restriction_changes>
> <region>coding</region>
> </RNA>
> <AA number="1" start="2" end="2" length="1" isMutation="1">
> <label>substitution</label>
> <label>conservative</label>
> <proof>computed</proof>
> <allele_ori>E</allele_ori>
> <allele_mut>K</allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+14T>A" trivname="L5X">
> <DNA number="1" start="14" end="14" length="1" isMutation="1">
> <label>point</label>
> <label>transversion</label>
> <proof>computed</proof>
> <upFlank>ccaagctcaaggatggaagtgcagt</upFlank>
> <allele_ori>t</allele_ori>
> <allele_mut>a</allele_mut>
> <dnFlank>agggctgggaagggtctaccctcgg</dnFlank>
> </DNA>
> <RNA number="1" start="14" end="14" length="1" isMutation="1">
> <label>nonsense</label>
> <proof>experimental</proof>
> <upFlank>ccaagctcaaggatggaagtgcagt</upFlank>
> <allele_ori>t</allele_ori>
> <allele_mut>a</allele_mut>
> <dnFlank>agggctgggaagggtctaccctcgg</dnFlank>
> <codon codon_ori="tta" codon_mut="taa" codon_pos="2"></codon>
> <region>coding</region>
> </RNA>
> <AA number="1" start="5" end="5" length="1" isMutation="1">
> <label>truncation</label>
> <proof>computed</proof>
> <allele_ori>L</allele_ori>
> <allele_mut>*</allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+4G>A" trivname="E2K">
> <DNA number="1" start="4" end="4" length="1" isMutation="1">
> <label>point</label>
> <label>transition</label>
> <proof>computed</proof>
> <upFlank>gaagattcagccaagctcaaggatg</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>a</allele_mut>
> <dnFlank>aagtgcagttagggctgggaagggt</dnFlank>
> <restriction_changes>-BccI</restriction_changes>
> </DNA>
> <RNA number="1" start="4" end="4" length="1" isMutation="1">
> <label>missense</label>
> <proof>experimental</proof>
> <upFlank>gaagattcagccaagctcaaggatg</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>a</allele_mut>
> <dnFlank>aagtgcagttagggctgggaagggt</dnFlank>
> <codon codon_ori="gaa" codon_mut="aaa" codon_pos="1"></codon>
> <restriction_changes>-BccI</restriction_changes>
> <region>coding</region>
> </RNA>
> <AA number="1" start="2" end="2" length="1" isMutation="1">
> <label>substitution</label>
> <label>conservative</label>
> <proof>computed</proof>
> <allele_ori>E</allele_ori>
> <allele_mut>K</allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+100delATCCAG" trivname="I34del-2">
> <DNA number="1" start="100" end="105" length="6" isMutation="1">
> <label>deletion</label>
> <proof>computed</proof>
> <upFlank>tctgttccagagcgtgcgcgaagtg</upFlank>
> <allele_ori>atccag</allele_ori>
> <allele_mut></allele_mut>
> <dnFlank>aacccgggccccaggcacccagagg</dnFlank>
> <restriction_changes>-BinI, -BsiYI, -DpnI, -Hpy178III, -MboI, +MjaIV</restriction_changes>
> </DNA>
> <RNA number="1" start="100" end="105" length="6" isMutation="1">
> <label>inframe</label>
> <label>deletion</label>
> <proof>experimental</proof>
> <upFlank>tctgttccagagcgtgcgcgaagtg</upFlank>
> <allele_ori>atccag</allele_ori>
> <allele_mut></allele_mut>
> <dnFlank>aacccgggccccaggcacccagagg</dnFlank>
> <codon codon_ori="atc" codon_pos="1"></codon>
> <restriction_changes>-BinI, -BsiYI, -DpnI, -Hpy178III, -MboI, +MjaIV</restriction_changes>
> <region>coding</region>
> </RNA>
> <AA number="1" start="34" end="35" length="2" isMutation="1">
> <label>deletion</label>
> <proof>computed</proof>
> <allele_ori>IQ</allele_ori>
> <allele_mut></allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+101delT" trivname="I34delX172">
> <DNA number="1" start="101" end="101" length="1" isMutation="1">
> <label>deletion</label>
> <proof>computed</proof>
> <upFlank>ctgttccagagcgtgcgcgaagtga</upFlank>
> <allele_ori>t</allele_ori>
> <allele_mut></allele_mut>
> <dnFlank>ccagaacccgggccccaggcaccca</dnFlank>
> <restriction_changes>-BinI, -DpnI, -Hpy178III, +MaeIII, -MboI, +Tsp45I</restriction_changes>
> </DNA>
> <RNA number="1" start="101" end="101" length="1" isMutation="1">
> <label>frameshift</label>
> <label>deletion</label>
> <proof>experimental</proof>
> <upFlank>ctgttccagagcgtgcgcgaagtga</upFlank>
> <allele_ori>t</allele_ori>
> <allele_mut></allele_mut>
> <dnFlank>ccagaacccgggccccaggcaccca</dnFlank>
> <codon codon_ori="atc" codon_pos="2"></codon>
> <restriction_changes>-BinI, -DpnI, -Hpy178III, +MaeIII, -MboI, +Tsp45I</restriction_changes>
> <region>coding</region>
> </RNA>
> <AA number="1" start="34" end="34" length="1" isMutation="1">
> <label>out-of-frame translation</label>
> <label>truncation</label>
> <proof>computed</proof>
> <allele_ori>I</allele_ori>
> <allele_mut>TRTRAPGTQRPRAQHLPAPVCCCCSSSSSSSSSSSSSSSSSSSSKRLAPGSSSSSRVRMVLPKPIVEAPQATWSWMRNSNLHSRSRPWSATPREVASQSLEPPWPPARGCRSSCQHLRTRMTQLPHPRCPCWAPLSPA*</allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+101insGGGCCC" trivname="I34ins+2">
> <DNA number="1" start="101" end="101" length="0" isMutation="1">
> <label>insertion</label>
> <proof>computed</proof>
> <upFlank>ctgttccagagcgtgcgcgaagtga</upFlank>
> <allele_ori></allele_ori>
> <allele_mut>gggccc</allele_mut>
> <dnFlank>tccagaacccgggccccaggcaccc</dnFlank>
> <restriction_changes>+ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +GsuI, +HaeIII, +HgiJII, -MboI, +MnlI, +NlaIV, +SduI</restriction_changes>
> </DNA>
> <RNA number="1" start="101" end="101" length="0" isMutation="1">
> <label>inframe</label>
> <label>insertion</label>
> <proof>experimental</proof>
> <upFlank>ctgttccagagcgtgcgcgaagtga</upFlank>
> <allele_ori></allele_ori>
> <allele_mut>gggccc</allele_mut>
> <dnFlank>tccagaacccgggccccaggcaccc</dnFlank>
> <codon codon_ori="atc" codon_pos="2"></codon>
> <restriction_changes>+ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +GsuI, +HaeIII, +HgiJII, -MboI, +MnlI, +NlaIV, +SduI</restriction_changes>
> <region>coding</region>
> </RNA>
> <AA number="1" start="34" end="34" length="1" isMutation="1">
> <label>insertion</label>
> <label>complex</label>
> <proof>computed</proof>
> <allele_ori>I</allele_ori>
> <allele_mut>RAL</allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+100insG" trivname="I34ins81X">
> <DNA number="1" start="100" end="100" length="0" isMutation="1">
> <label>insertion</label>
> <proof>computed</proof>
> <upFlank>tctgttccagagcgtgcgcgaagtg</upFlank>
> <allele_ori></allele_ori>
> <allele_mut>g</allele_mut>
> <dnFlank>atccagaacccgggccccaggcacc</dnFlank>
> <restriction_changes>+BamHI, +BinI, +NlaIV, +XhoII</restriction_changes>
> </DNA>
> <RNA number="1" start="100" end="100" length="0" isMutation="1">
> <label>frameshift</label>
> <label>insertion</label>
> <proof>experimental</proof>
> <upFlank>tctgttccagagcgtgcgcgaagtg</upFlank>
> <allele_ori></allele_ori>
> <allele_mut>g</allele_mut>
> <dnFlank>atccagaacccgggccccaggcacc</dnFlank>
> <codon codon_ori="atc" codon_pos="1"></codon>
> <restriction_changes>+BamHI, +BinI, +NlaIV, +XhoII</restriction_changes>
> <region>coding</region>
> </RNA>
> <AA number="1" start="34" end="34" length="1" isMutation="1">
> <label>out-of-frame translation</label>
> <label>truncation</label>
> <proof>computed</proof>
> <allele_ori>I</allele_ori>
> <allele_mut>DPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*</allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+100AT>GGGCCC" trivname="I34ins82X">
> <DNA number="1" start="100" end="101" length="2" isMutation="1">
> <label>complex</label>
> <proof>computed</proof>
> <upFlank>tctgttccagagcgtgcgcgaagtg</upFlank>
> <allele_ori>at</allele_ori>
> <allele_mut>gggccc</allele_mut>
> <dnFlank>ccagaacccgggccccaggcaccca</dnFlank>
> <restriction_changes>+ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +HaeIII, +HgiJII, -Hpy178III, -MboI, +NlaIV, +SduI</restriction_changes>
> </DNA>
> <RNA number="1" start="100" end="101" length="2" isMutation="1">
> <label>frameshift</label>
> <label>complex</label>
> <proof>experimental</proof>
> <upFlank>tctgttccagagcgtgcgcgaagtg</upFlank>
> <allele_ori>at</allele_ori>
> <allele_mut>gggccc</allele_mut>
> <dnFlank>ccagaacccgggccccaggcaccca</dnFlank>
> <codon codon_ori="atc" codon_pos="1"></codon>
> <restriction_changes>+ApaI, +AsuI, -BinI, +BmgI, +BseSI, +CviJI, -DpnI, +DraII, +HaeIII, +HgiJII, -Hpy178III, -MboI, +NlaIV, +SduI</restriction_changes>
> <region>coding</region>
> </RNA>
> <AA number="1" start="34" end="34" length="1" isMutation="1">
> <label>out-of-frame translation</label>
> <label>truncation</label>
> <proof>computed</proof>
> <allele_ori>I</allele_ori>
> <allele_mut>GPPEPGPQAPRGRERSTSRRQFAAAAAAAAAAAAAAAAAAAAAAAARD*</allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.-1G>A">
> <DNA number="1" start="-1" end="-1" length="1" isMutation="1">
> <label>point</label>
> <label>transition</label>
> <proof>computed</proof>
> <upFlank>ggtggaagattcagccaagctcaag</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>a</allele_mut>
> <dnFlank>atggaagtgcagttagggctgggaa</dnFlank>
> <restriction_changes>-BccI, -FokI, +Hpy178III</restriction_changes>
> </DNA>
> <RNA number="1" start="-1" end="-1" length="1" isMutation="1">
> <label>unknown</label>
> <proof>experimental</proof>
> <upFlank>ggtggaagattcagccaagctcaag</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>a</allele_mut>
> <dnFlank>atggaagtgcagttagggctgggaa</dnFlank>
> <restriction_changes>-BccI, -FokI, +Hpy178III</restriction_changes>
> <region>5'UTR</region>
> </RNA>
> </seqDiff>
> <seqDiff id="M20132" moltype="rna" offset="362" sysname="c.+2766T>C">
> <DNA number="1" start="2766" end="2766" length="1" isMutation="1">
> <label>point</label>
> <label>transition</label>
> <proof>computed</proof>
> <upFlank>tctatttccacacccagtgaagcat</upFlank>
> <allele_ori>t</allele_ori>
> <allele_mut>c</allele_mut>
> <dnFlank>ggaaaccctatttccccaccccagc</dnFlank>
> <restriction_changes>+Hpy188I, +SfaNI, -XcmI</restriction_changes>
> </DNA>
> <RNA number="1" start="2766" end="2766" length="1" isMutation="1">
> <label>unknown</label>
> <proof>experimental</proof>
> <upFlank>tctatttccacacccagtgaagcat</upFlank>
> <allele_ori>t</allele_ori>
> <allele_mut>c</allele_mut>
> <dnFlank>ggaaaccctatttccccaccccagc</dnFlank>
> <restriction_changes>+Hpy188I, +SfaNI, -XcmI</restriction_changes>
> <region>3'UTR</region>
> </RNA>
> </seqDiff>
> <seqDiff id="J02933" moltype="dna" offset="521" sysname="g.+12165A>G">
> <DNA number="1" start="12165" end="12165" length="1" isMutation="1">
> <label>point</label>
> <label>transition</label>
> <proof>experimental</proof>
> <upFlank>cgcacacctgtggtgcctgccaccc</upFlank>
> <allele_ori>a</allele_ori>
> <allele_mut>g</allele_mut>
> <dnFlank>ctgggttgcccatgattcatttttg</dnFlank>
> <restriction_changes>+AciI, -BfiI, -BsrI, +FauI, +NspBII, +Sth132I, -TspRI</restriction_changes>
> <region dist="1027">3'UTR</region>
> </DNA>
> <RNA number="1" start="2428" end="2428" length="1" isMutation="1">
> <label>unknown</label>
> <proof>computed</proof>
> <upFlank>cgcacacctgtggtgcctgccaccc</upFlank>
> <allele_ori>a</allele_ori>
> <allele_mut>g</allele_mut>
> <dnFlank>ctgggttgcccatgattcatttttg</dnFlank>
> <restriction_changes>+AciI, -BfiI, -BsrI, +FauI, +NspBII, +Sth132I, -TspRI</restriction_changes>
> <region dist="-1">3'UTR</region>
> </RNA>
> </seqDiff>
> <seqDiff id="J02933" moltype="dna" offset="521" sysname="g.+4G>T" trivname="V2F">
> <DNA number="1" start="4" end="4" length="1" isMutation="1">
> <label>point</label>
> <label>transversion</label>
> <proof>computed</proof>
> <upFlank>gcagcactgcagagatttcatcatg</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>t</allele_mut>
> <dnFlank>tctcccaggccctcaggctcctctg</dnFlank>
> <restriction_changes>-BsmAI, -Eco31I</restriction_changes>
> <region value="1" dist="4">exon</region>
> </DNA>
> <RNA number="1" start="4" end="4" length="1" isMutation="1">
> <label>missense</label>
> <proof>experimental</proof>
> <upFlank>gcagcactgcagagatttcatcatg</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>t</allele_mut>
> <dnFlank>tctcccaggccctcaggctcctctg</dnFlank>
> <codon codon_ori="gtc" codon_mut="ttc" codon_pos="1"></codon>
> <restriction_changes>-BsmAI, -Eco31I</restriction_changes>
> <region>coding</region>
> </RNA>
> <AA number="1" start="2" end="2" length="1" isMutation="1">
> <label>substitution</label>
> <label>nonconservative</label>
> <proof>computed</proof>
> <allele_ori>V</allele_ori>
> <allele_mut>F</allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="J02933" moltype="dna" offset="521" sysname="g.+1168G>T" trivname="D34Y">
> <DNA number="1" start="1168" end="1168" length="1" isMutation="1">
> <label>point</label>
> <label>transversion</label>
> <proof>computed</proof>
> <upFlank>taaggcctcaggaggagaaacacgg</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>t</allele_mut>
> <dnFlank>acatgccgtggaagccggggcctca</dnFlank>
> <restriction_changes>-BscGI, -Bsp24I, -CjePI, -FinI, +RsaI, -Sth132I, +Tsp4CI</restriction_changes>
> <region value="1" dist="-29">exon</region>
> </DNA>
> <RNA number="1" start="100" end="100" length="1" isMutation="1">
> <label>missense</label>
> <proof>experimental</proof>
> <upFlank>taaggcctcaggaggagaaacacgg</upFlank>
> <allele_ori>g</allele_ori>
> <allele_mut>t</allele_mut>
> <dnFlank>acatgccgtggaagccggggcctca</dnFlank>
> <codon codon_ori="gac" codon_mut="tac" codon_pos="1"></codon>
> <restriction_changes>-BscGI, -Bsp24I, -CjePI, -FinI, +RsaI, -Sth132I, +Tsp4CI</restriction_changes>
> <region>coding</region>
> </RNA>
> <AA number="1" start="34" end="34" length="1" isMutation="1">
> <label>substitution</label>
> <label>nonconservative</label>
> <proof>computed</proof>
> <allele_ori>D</allele_ori>
> <allele_mut>Y</allele_mut>
> </AA>
> </seqDiff>
> <seqDiff id="J02933" moltype="dna" offset="521" sysname="g.-4C>G">
> <DNA number="1" start="-4" end="-4" length="1" isMutation="1">
> <label>point</label>
> <label>transversion</label>
> <proof>computed</proof>
> <upFlank>ggcaggggcagcactgcagagattt</upFlank>
> <allele_ori>c</allele_ori>
> <allele_mut>g</allele_mut>
> <dnFlank>atcatggtctcccaggccctcaggc</dnFlank>
> <restriction_changes>+BclI, +DpnI, +MboI</restriction_changes>
> <region dist="-4">5'UTR</region>
> </DNA>
> <RNA number="1" start="-4" end="-4" length="1" isMutation="1">
> <label>unknown</label>
> <proof>experimental</proof>
> <upFlank>ggcaggggcagcactgcagagattt</upFlank>
> <allele_ori>c</allele_ori>
> <allele_mut>g</allele_mut>
> <dnFlank>atcatggtctcccaggccctcaggc</dnFlank>
> <restriction_changes>+BclI, +DpnI, +MboI</restriction_changes>
> <region dist="31">5'UTR</region>
> </RNA>
> </seqDiff>
Failed 3/25 subtests
t/WABA.........................ok
t/XEMBL_DB.....................SOAP::Lite and/or XML::DOM not installed. This means that Bio::DB::XEMBL module is not usable. Skipping tests.
ok
Test Summary Report
-------------------
t/Biblio.t (Wstat: 0 Tests: 24 Failed: 0)
Tests skipped: 2
t/BioFetch_DB.t (Wstat: 0 Tests: 27 Failed: 1)
Failed tests: 8
t/EMBL_DB.t (Wstat: 0 Tests: 15 Failed: 3)
Failed tests: 6, 13-14
t/Genewise.t (Wstat: 0 Tests: 51 Failed: 0)
Tests skipped: 33-34
t/GuessSeqFormat.t (Wstat: 0 Tests: 46 Failed: 1)
Failed tests: 11
t/InterProParser.t (Wstat: 512 Tests: 47 Failed: 1)
Failed tests: 2
Non-zero exit status: 2
t/MeSH.t (Wstat: 0 Tests: 26 Failed: 1)
Failed tests: 26
t/Ontology.t (Wstat: 2304 Tests: 0 Failed: 0)
Non-zero exit status: 9
Parse errors: Bad plan. You planned 50 tests but ran 0.
t/RemoteBlast.t (Wstat: 0 Tests: 6 Failed: 0)
Tests skipped: 3-6
t/SeqIO.t (Wstat: 0 Tests: 235 Failed: 0)
Tests skipped: 68, 114, 126
t/simpleGOparser.t (Wstat: 2304 Tests: 0 Failed: 0)
Non-zero exit status: 9
Parse errors: Bad plan. You planned 98 tests but ran 0.
t/Taxonomy.t (Wstat: 0 Tests: 8 Failed: 0)
Tests skipped: 2-8
t/tutorial.t (Wstat: 512 Tests: 18 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 21 tests but ran 18.
t/Variation_IO.t (Wstat: 0 Tests: 25 Failed: 3)
Failed tests: 15, 20, 25
Files=179, Tests=8122, 323 wallclock secs (200.36 cusr + 7.74 csys = 208.10 CPU)
Result: FAIL
Failed 9/179 test programs. 10/8122 subtests failed.
make: *** [test_dynamic] Error 255
--
Summary of my perl5 (revision 5 version 8 subversion 5) configuration:
Platform:
osname=linux, osvers=2.6.18-4-k7, archname=i686-linux-thread-multi-64int
uname='linux k75 2.6.18-4-k7 #1 smp mon mar 26 17:57:15 utc 2007 i686 gnulinux '
config_args='-Dprefix=/home/src/perl/repoperls/installed-perls/maint-5.8/pOrDlAM/perl-5.8.0@23390 -Dinstallusrbinperl=n -Uversiononly -des -Dusethreads -Duse64bitint -Dusedevel -Doptimize=-g -Dnoextensions=Encode'
hint=recommended, useposix=true, d_sigaction=define
usethreads=define use5005threads=undef useithreads=define usemultiplicity=define
useperlio=define d_sfio=undef uselargefiles=define usesocks=undef
use64bitint=define use64bitall=undef uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-g',
cppflags='-D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include'
ccversion='', gccversion='4.1.2 20061115 (prerelease) (Debian 4.1.1-21)', gccosandvers=''
intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=12345678
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12
ivtype='long long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=4, prototype=define
Linker and Libraries:
ld='cc', ldflags =' -L/usr/local/lib'
libpth=/usr/local/lib /lib /usr/lib
libs=-lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lpthread -lc
perllibs=-lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
libc=/lib/libc-2.3.6.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.3.6'
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
cccdlflags='-fpic', lddlflags='-shared -L/usr/local/lib'
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