[Biojava-l] Genbank parser error [biojavax]
Morgane THOMAS-CHOLLIER
mthomasc at vub.ac.be
Tue Feb 14 08:33:02 EST 2006
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
**********************************************************
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