[Biojava-l] Genbank parser error [biojavax]
mark.schreiber at novartis.com
mark.schreiber at novartis.com
Wed Feb 15 04:00:44 EST 2006
Hi Morgane -
Turned out to be a problem with a greedy regexp parsing the LOCUS tag.
This is fixed in CVS. Let me know if something else is a problem.
- Mark
Morgane THOMAS-CHOLLIER <mthomasc at vub.ac.be>
Sent by: biojava-l-bounces at portal.open-bio.org
02/14/2006 09:33 PM
To: biojava-l at biojava.org
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: Re: [Biojava-l] Genbank parser error [biojavax]
Hello Mark,
My file is indeed too large to be posted.
So I have exported a smaller sequence from Ensembl that I tested with
the parser. The behavior is the same.
You will find below this "Genbank" formatted file enclosed.
Thanks for your help,
Morgane.
LOCUS 6 3498 bp DNA HTG 14-FEB-2006
DEFINITION Mus musculus chromosome 6 NCBIM34 partial sequence
52305503..52309000 reannotated via EnsEMBL
ACCESSION chromosome:NCBIM34:6:52305503:52309000:1
VERSION chromosome:NCBIM34:6:52305503:52309000:1
KEYWORDS .
SOURCE House mouse
ORGANISM Mus musculus
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
Sciurognathi; Muridae; Murinae; Mus.
COMMENT This sequence was annotated by the Ensembl system. Please
visit the
Ensembl web site, http://www.ensembl.org/ for more information.
COMMENT All feature locations are relative to the first (5') base of
the
sequence in this file. The sequence presented is always the
forward strand of the assembly. Features that lie outside of
the
sequence contained in this file have clonal location
coordinates in
the format: .:..
COMMENT The /gene indicates a unique id for a gene,
/note="transcript_id=..." a unique id for a transcript,
/protein_id
a unique id for a peptide and note="exon_id=..." a unique id
for an
exon. These ids are maintained wherever possible between
versions.
COMMENT All the exons and transcripts in Ensembl are confirmed by
similarity to either protein or cDNA sequences.
FEATURES Location/Qualifiers
source 1..3498
/organism="Mus musculus"
/db_xref="taxon:10090"
gene complement(506..2826)
/gene=ENSMUSG00000014704
mRNA join(complement(2261..2826),complement(506..1620))
/gene="ENSMUSG00000014704"
/note="transcript_id=ENSMUST00000014848"
CDS join(complement(2261..2639),complement(881..1620))
/gene="ENSMUSG00000014704"
/protein_id="ENSMUSP00000014848"
/note="transcript_id=ENSMUST00000014848"
/db_xref="MarkerSymbol:Hoxa2"
/db_xref="Uniprot/SWISSPROT:HXA2_MOUSE"
/db_xref="RefSeq_peptide:NP_034581.1"
/db_xref="RefSeq_dna:NM_010451.1"
/db_xref="Uniprot/SPTREMBL:Q3UYP9_MOUSE"
/db_xref="Uniprot/SPTREMBL:Q920T7_MOUSE"
/db_xref="Uniprot/SPTREMBL:Q920T9_MOUSE"
/db_xref="Uniprot/SPTREMBL:Q920U0_MOUSE"
/db_xref="Uniprot/SPTREMBL:Q920U1_MOUSE"
/db_xref="Uniprot/SPTREMBL:Q920U2_MOUSE"
/db_xref="Uniprot/SPTREMBL:Q920U3_MOUSE"
/db_xref="Uniprot/SPTREMBL:Q920U4_MOUSE"
/db_xref="Uniprot/SPTREMBL:Q920U5_MOUSE"
/db_xref="EntrezGene:15399"
/db_xref="AgilentProbe:A_51_P501803"
/db_xref="EMBL:AB039184"
/db_xref="EMBL:AB039185"
/db_xref="EMBL:AB039186"
/db_xref="EMBL:AB039187"
/db_xref="EMBL:AB039188"
/db_xref="EMBL:AB039189"
/db_xref="EMBL:AB039190"
/db_xref="EMBL:AB039191"
/db_xref="EMBL:AB039192"
/db_xref="EMBL:AK134501"
/db_xref="EMBL:M87801"
/db_xref="EMBL:M93148"
/db_xref="EMBL:M93292"
/db_xref="EMBL:M95599"
/db_xref="GO:GO:0003700"
/db_xref="GO:GO:0005634"
/db_xref="GO:GO:0006355"
/db_xref="GO:GO:0007275"
/db_xref="IPI:IPI00132242.1"
/db_xref="UniGene:Mm.131"
/db_xref="protein_id:AAA37827.1"
/db_xref="protein_id:AAA37834.1"
/db_xref="protein_id:AAA37835.1"
/db_xref="protein_id:AAA37836.1"
/db_xref="protein_id:BAB68708.1"
/db_xref="protein_id:BAB68709.1"
/db_xref="protein_id:BAB68710.1"
/db_xref="protein_id:BAB68711.1"
/db_xref="protein_id:BAB68712.1"
/db_xref="protein_id:BAB68713.1"
/db_xref="protein_id:BAB68714.1"
/db_xref="protein_id:BAB68715.1"
/db_xref="protein_id:BAB68716.1"
/db_xref="protein_id:BAE22163.1"
/db_xref="AFFY_MG_U74Av2:102643_at"
/db_xref="AFFY_MG_U74Cv2:171063_at"
/db_xref="AFFY_Mouse430A_2:1419602_at"
/db_xref="AFFY_Mouse430_2:1419602_at"
/translation="MNYEFEREIGFINSQPSLAECLTSFPPVADTFQSSSIKTSTLSH
STLIPPPFEQTIPSLNPGSHPRHGAGVGGRPKSSPAGSRGSPVPAGALQPPEYPWMKE
KKAAKKTALPPAAASTGPACLGHKESLEIADGSGGGSRRLRTAYTNTQLLELEKEFHF
NKYLCRPRRVEIAALLDLTERQVKVWFQNRRMKHKRQTQCKENQNSEGKFKNLEDSDK
VEEDEEEKSLFEQALSVSGALLEREGYTFQQNALSQQQAPNGHNGDSQTFPVSPLTSN
EKNLKHFQHQSPTVPNCLSTMGQNCGAGLNNDSPEAIEVPSLQDFNVFSTDSCLQLSD
ALSPSLPGSLDSPVDISADSFDFFTDTLTTIDLQHLNY"
exon complement(506..1620)
/note="exon_id=ENSMUSE00000387033"
exon complement(2261..2826)
/note="exon_id=ENSMUSE00000193269"
BASE COUNT 938 a 815 c 882 g 863 t
ORIGIN
1 AGGAAGAGTT GGAACGTAGA TGTTTGAAAC AAATGTGTAT AAATAAATGA
ATTTTTGATA
61 ACTCCGTTAT TGACCTAGAA ACTAGCAGCT TGGTAAGGGA ACTCCATTCC
ACTCCACTCG
121 TCCTAGAACT GGAAGTTTTT GTAGGCACTT TTCCTCTCCA CACTCAAAAG
CTTGGGCTAG
181 GGCCAACTCA GGCTGCCCAA GCCCATTTCT ATTACTAATG TAACTCTATG
GCCTGAGTCT
241 CAACACTGAA AACCAAATTC ATTCCCTTAG GGGGGAAAAA TCCAAAAAAA
AAAAAAAAAA
301 AAGTCTTGCC AGAAGCCCTA GCACTTTCTG GTTTTCTTCT TTGTTGCTGT
TTGTTGCAGG
361 CTTTGAACAT GCCACCCTAA TAAAATATAT TAAGATTGAA AAGTAAATTG
TGACCAGACT
421 TTTATTTACC ATGTTAGACT AAAAGAAGTA TAAGAAATCA GTATGAGTCT
TGAGAAAGAG
481 GGGAAGAAAA AAATAAGAAA GCTACTTATA GCAAAGGAGA ATTTATTCTA
CCAAAAATAC
541 GCATGACAAT GCATTCTAAT GTGGTACAAA AATAAACAGA AAGTGACAAG
ACAATTTATG
601 GTCACTTTCT TGCAGGCCTC CTGTTTTGTT TTTCAGGAAA ATCACATAGA
AGCTTGTTGG
661 GTTCTGTGTA AAAACCACTT AGAACGCCAA CATAATTTGC AAGAGATGGC
TTTAAAACTG
721 TGTCAGGGGA GAACATTAAA CGGAAAGTCC TCAACATTTG AGAGAGTAGG
GGTAGATCAA
781 GAAGAAACTA AAACGAAAAT CAACTCCCAG AATAAAAGAA GGCAAAGCCA
CCTGGTCAAA
841 GGCGTTTTGT TTTGTGAAGC TTTGTTTTGC TTTAATGTTC TTAGTAATTC
AGATGCTGTA
901 GGTCGATTGT GGTGAGTGTG TCTGTAAAAA AGTCAAAGCT GTCAGCTGAG
ATATCTACAG
961 GACTGTCCAG GGAGCCAGGC AAGCTGGGCG ACAGTGCATC TGAAAGCTGC
AGGCAGGAAT
1021 CTGTGGAGAA AACATTGAAG TCCTGCAAAG AGGGGACCTC GATGGCCTCG
GGACTGTCAT
1081 TGTTTAGGCC AGCTCCACAG TTCTGGCCCA TTGTTGACAA GCAGTTAGGA
ACAGTGGGTG
1141 ACTGGTGCTG AAAATGTTTC AAATTTTTCT CATTGCTGGT TAAAGGCGAA
ACTGGGAAAG
1201 TTTGGGAGTC GCCATTGTGT CCATTGGGAG CCTGCTGTTG AGAGAGCGCA
TTTTGCTGAA
1261 AAGTGTACCC TTCCCTCTCC AGAAGGGCCC CGGAGACACT GAGGGCTTGC
TCAAAGAGTG
1321 ACTTCTCTTC CTCGTCTTCC TCCACTTTGT CCGAGTCCTC CAGGTTTTTA
AATTTCCCTT
1381 CGCTGTTTTG GTTCTCCTTG CACTGGGTTT GCCTCTTATG CTTCATTCTC
CGGTTCTGAA
1441 ACCACACTTT CACTTGTCTC TCGGTCAAAT CCAGCAGCGC GGCGATTTCC
ACCCTGCGGG
1501 GTCTGCAAAG GTACTTGTTG AAATGAAATT CCTTTTCCAG CTCCAAAAGC
TGAGTGTTGG
1561 TGTACGCGGT TCTCAGACGC CTGGATCCCC CGCCGCTGCC ATCAGCTATT
TCCAGGGATT
1621 CTGCAGAAAG GGAAACCAAC AAGAGACACA CATACAGTTG AAGGTGGAAG
GGTCCGAGCA
1681 GGGTTATTCC ATTGGAGCAT AAATACAGCA GAAAAGATCA ACTGCAACAA
AATGGCCGCC
1741 CCTGGATGCA GTGCAGCTAT TGTGCTGCCC TTCCTGGGAG CCCAGCCCGG
GGAAGCCCAG
1801 TCTCTTCCAC CTCCATCAAA TTCCTGCCTG TGGCTTCCCC CAACCTCTTC
ATCCGGGAGC
1861 AAACTTTATA TTAGCTACAA CACAATTTAT AATTAATGCA TCAGCTGCTT
AGCTGAGCAA
1921 GAGCGGTCTA TCACTCTTCA TTACTGTCAA AAAGCCAAAC TCTAGGACAA
CTAGACAAGA
1981 GGAGGTCAGT TCCAACTCAA ATAAATCATC CTACATTACA CAAGTTAGGG
AAAGTGCCCC
2041 CCCTCCTCAA AATATATATG TCTCATTGTG GGACTCGGGA TCTATTTTCC
CCTCCACCAA
2101 ACCCACTCCT GAGACCACAG GGGCATGAGA CCCGCCACCA GGCATCTCTC
TCTCTCCCCC
2161 TTCCCTCGAA GCTCATGGTC CCCTCCCCCA CAACCGCTCC TAGGGAAGCC
CGGAGGGGGA
2221 CAAGGGTCCC CGAGACCTGG GGCCAAGTCT CCGGACTGAC CTTTGTGGCC
GAGGCAGGCA
2281 GGGCCCGTGG AGGCGGCGGC GGGCGGCAGC GCGGTTTTCT TGGCCGCCTT
CTTCTCCTTC
2341 ATCCAGGGAT ACTCAGGCGG CTGCAGGGCG CCGGCAGGCA CCGGGCTGCC
GCGACTGCCC
2401 GCGGGGCTCG ACTTGGGGCG GCCGCCAACG CCAGCGCCGT GGCGAGGGTG
ACTGCCCGGG
2461 TTCAGGCTGG GAATGGTCTG CTCAAAAGGA GGAGGAATCA GTGTCGAGTG
TGAAAGCGTC
2521 GAGGTCTTGA TTGATGAACT TTGAAATGTA TCAGCGACAG GGGGAAAAGA
TGTCAGGCAC
2581 TCAGCGAGCG ACGGCTGGCT ATTGATAAAA CCAATCTCTC GCTCAAATTC
GTAATTCATG
2641 GCCTTCTCCT TGGAGCCCCC TCGGAGGAAA AGTTCCCTCT TTTGGAGGGG
CTTTGGGGGG
2701 GCAAGGCCCA GGAAAAAGGC GAGCGCGAAG GAAAAAAAAA TCTATCATAG
AAGATCGCTG
2761 CTGGGGTGTT TTTTTTCTAA TTCACTGATT ACAGCCGTAT GGGGACCGCG
CTACTATTAA
2821 ACTATTGAAT TCATGGAGAC AAGGTTGAAA TTGGACCGAA TTGGCTGTCA
CATGATTGCT
2881 TCTGCCCAAT GACAATTTGG GCTTTAATCA AAAGAAGCCA CTGTCTGTTT
GATTGATCCA
2941 AAAAAGTCAG AAAGGAACGC CTCATTGGGG GCCATCGAGG CTTTATTTAC
ACTTTTTTTC
3001 AGGGCAAAAA TACATATATG TGGGTGTGGA TGGCAATGCC CCGGGAGTGC
GTGGGGGGCG
3061 AGAGTGCCTG TTTGCCTCCT GATCTGCAAG GATCTAGTGT GCTCCCTGGA
GTGTGTGTGT
3121 GAGTGTGTGC GTGTGAGCCC TGCTGCCGTC CCGCCAGTGG CTGCCCTCTG
CCTCCCCCGC
3181 ACACTCCGCG CATTGTTTGG GACTGTCGGG AAGACGCCTC GCACCTCACA
AATCATTTAA
3241 GCACCTCAGC CTGACGCCTG CAGTCATTAA CAAAGTAATC CATTAATCTT
CAAAGTTTTG
3301 ACACCCCAGG GCCCTGCATC TCAGCCACAT AAGTTCTGCT AAGGCAAGAG
AAAGGAGCAG
3361 AGTGGGAGAG AGAGAGGAGA GAGGGAGAGA GGGAGAGAGG GAGAGAGAGA
GAGAGAGAGA
3421 GAGAGAGAGA GAGAGAGAGA GAGAGAATGA ATATTGGGGT TCACCTTTCC
TCTTCCTCCT
3481 CTTTTTCCAA AATCAGTT
//
mark.schreiber at novartis.com wrote:
>Hi Morgane -
>
>I have to say that doesn't look much like Genbank : )
>
>The biojavax parser are possibly a bit brittle due to their use of
regexps
>to recognize key elements. It should be fixable, I think the problem is
>that the parser expects a word after LOCUS not a number. This may not be
>the only problem though. Could you post the entire file? Or if it is
large
>then a representative file of smaller size.
>
>- Mark
>
>
>
>
>
>Morgane THOMAS-CHOLLIER <mthomasc at vub.ac.be>
>Sent by: biojava-l-bounces at portal.open-bio.org
>02/14/2006 04:36 AM
>
>
> To: biojava-l at biojava.org
> cc: (bcc: Mark Schreiber/GP/Novartis)
> Subject: [Biojava-l] Genbank parser error [biojavax]
>
>
>Hello,
>
>I have tried biojavax today with a view to use the Genbank file parser.
>
>My test file is a Genbank formatted file which has been produced by
>Ensembl export system.
>
>The head of the file is as follow :
>
>LOCUS 6 489671 bp DNA HTG 13-FEB-2006
>DEFINITION Mus musculus chromosome 6 NCBIM34 partial sequence
> 52296503..52786173 reannotated via EnsEMBL
>ACCESSION chromosome:NCBIM34:6:52296503:52786173:1
>VERSION chromosome:NCBIM34:6:52296503:52786173:1
>
>I used the code provided in biojavax docbook to parse this file.
>I get the following error :
>
>Exception in thread "main" org.biojava.bio.BioException: Could not read
>sequence
> at
>org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:111)
> at
>org.embnet.be.biojavax.tryout.GenbankParseTest.main(GenbankParseTest.java:31)
>Caused by: org.biojava.bio.seq.io.ParseException: Bad locus line found:
>6 489671 bp DNA HTG 13-FEB-2006
> at
>org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:229)
> at
>org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:108)
> ... 1 more
>
>I had a look at GenbankFormat.java, and I guess the problem comes from
>the regular expression that do not recognize the LOCUS as a standard
>Genbank file LOCUS tag.
>
>Am I wrong ? Have biojavax Genbank parser been tested on Ensembl
>exported files ?
>
>Morgane.
>
>
>
--
**********************************************************
Morgane THOMAS-CHOLLIER, PHD Student (mthomasc at vub.ac.be)
Vrije Universiteit Brussels (VUB)
Laboratory of Cell Genetics
Pleinlaan 2
1050 Brussels
Belgium
Tel : +32 2 629 15 22
**********************************************************
Stop Using Internet Explorer, choose FIREFOX !
http://emmanuel.clement.free.fr/navigateurs/comparatif.htm
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