Running make test
PERL_DL_NONLAZY=1 /usr/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.....................ok                                              
t/Biblio_biofetch............ok                                              
t/BiblioReferences...........ok                                              
t/BioDBGFF...................ok                                              
t/BioFetch_DB................FAILED test 8                                   
        Failed 1/27 tests, 96.30% okay
t/BioGraphics................ok                                              
t/BlastIndex.................ok                                              
t/BPbl2seq...................ok                                              
t/BPlite.....................ok                                              
t/BPpsilite..................ok                                              
t/Chain......................ok                                              
t/cigarstring................ok                                              
t/ClusterIO..................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........................ok 1/14                                         
-------------------- WARNING ---------------------
MSG: Bio::Tools::Analysis::Protein::ELM Request Error:
400 URL must be absolute
Content-Type: text/plain
Client-Date: Mon, 13 Nov 2006 17:54:55 GMT
Client-Warning: Internal response

400 URL must be absolute

---------------------------------------------------
t/ELM........................ok                                              
t/EMBL_DB....................FAILED tests 6, 13-14                           
        Failed 3/15 tests, 80.00% okay
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.......................ok                                              
t/GDB........................ok                                              
t/GeneCoordinateMapper.......ok 1/113                                        
-------------------- 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 /private/var/root/.cpan/build/bioperl-1.4/blib/lib/Bio/Coordinate/GeneMapper.pm line 814.
t/GeneCoordinateMapper.......ok                                              
t/Geneid.....................ok                                              
t/Genewise...................ok                                              
        2/51 skipped: 
t/Genomewise.................ok                                              
t/Genpred....................ok                                              
t/GFF........................ok 1/32Filehandle GEN0 opened only for output at /private/var/root/.cpan/build/bioperl-1.4/blib/lib/Bio/Root/IO.pm line 440.
Filehandle GEN1 opened only for output at /private/var/root/.cpan/build/bioperl-1.4/blib/lib/Bio/Root/IO.pm line 440.
t/GFF........................ok                                              
t/GOR4.......................ok                                              
t/GOterm.....................ok                                              
t/GuessSeqFormat.............ok                                              
t/hmmer......................ok                                              
t/HNN........................ok                                              
t/Index......................ok                                              
t/InstanceSite...............ok                                              
t/InterProParser.............ok                                              
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.......................ok                                              
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 /Library/Perl/5.8.6/Graph.pm line 2381, <GEN0> line 10.
t/Ontology...................dubious                                         
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-50
        Failed 50/50 tests, 0.00% okay
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                                              
        4/6 skipped: to avoid timeout
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...................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                                              
        3/235 skipped: 
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 /Library/Perl/5.8.6/Graph.pm line 2381, <GEN1> line 14.
t/simpleGOparser.............dubious                                         
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-98
        Failed 98/98 tests, 0.00% okay
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                                              
        7/8 skipped: to avoid blocking
t/Tempfile...................ok                                              
t/Term.......................ok                                              
t/Tools......................ok                                              
t/Tree.......................ok                                              
t/TreeIO.....................FAILED test 42                                  
        Failed 1/41 tests, 97.56% okay
t/trim.......................ok                                              
t/tutorial...................ok 17/21Use of uninitialized value in print at /private/var/root/.cpan/build/bioperl-1.4/blib/lib/bptutorial.pl line 4042, <GEN20> line 934.
t/tutorial...................ok                                              
t/UCSCParsers................ok                                              
t/Unflattener................ok                                              
t/Unflattener2...............ok                                              
t/UniGene....................ok                                              
t/Variation_IO...............NOK 151d0   
< 
32d30
< 
60d57
< 
91d87
< 
121d116
< 
152d146
< 
183d176
< 
214d206
< 
245d236
< 
268d258
< 
291d280
< 
315d303
< 
347d334
< 
379d365
< 
t/Variation_IO...............NOK 201d0                                       
< 
t/Variation_IO...............NOK 251,350c1,388                               
< 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&gt;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&gt;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&gt;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&gt;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&gt;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&gt;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&gt;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&gt;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&gt;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&gt;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>
t/Variation_IO...............FAILED tests 15, 20, 25                         
        Failed 3/25 tests, 88.00% okay
t/WABA.......................ok                                              
t/XEMBL_DB...................ok                                              
Failed Test        Stat Wstat Total Fail  List of Failed
-------------------------------------------------------------------------------
t/BioFetch_DB.t                  27    1  8
t/EMBL_DB.t                      15    3  6 13-14
t/Ontology.t        255 65280    50  100  1-50
t/TreeIO.t                       41    1  42
t/Variation_IO.t                 25    3  15 20 25
t/simpleGOparser.t  255 65280    98  196  1-98
16 subtests skipped.
Failed 6/179 test scripts. 154/8273 subtests failed.
Files=179, Tests=8273, 103 wallclock secs (58.37 cusr +  6.43 csys = 64.80 CPU)
Failed 6/179 test programs. 154/8273 subtests failed.
make: *** [test_dynamic] Error 255
  /usr/bin/make test -- NOT OK
Running make install
Writing /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/.packlist
Appending installation info to /System/Library/Perl/5.8.6/darwin-thread-multi-2level/perllocal.pod
  /usr/bin/make install  -- OK
Failed during this command:
  BIRNEY/bioperl-1.4.tar.gz                    : make_test FAILED but failure ignored because 'force' in effect