[Biojava-l] Genbank parser error [biojavax]

mark.schreiber at novartis.com mark.schreiber at novartis.com
Wed Feb 15 07:20:13 EST 2006


I think these properties should be going to the (Rich)Annotation bundle.

- Mark





Morgane THOMAS-CHOLLIER <mthomasc at vub.ac.be>
Sent by: biojava-l-bounces at portal.open-bio.org
02/15/2006 04:56 PM

 
        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-l] Genbank  parser error [biojavax]


Hello again,

I have continued using the Genbank parser, but this time with Genbank 
files coming from NCBI :)

I really appreciate the example from the documentation that converts a 
Genbank file into an EMBL file. I have to say, it is really easy to use.

I nevertheless have a question concerning the Organism and Source tags. 
Indeed, it is clear in the documentation that they are ignored by the 
parser.
But I do not really understand why.
When I used the Genbank file of the accession numbers : AC147788 and 
DQ158013, I was unable to get the common name of the organism or use 
getNameHierarchy(), but I can get the taxon ID for both.

Is there a way to get the common name of the organism, without using a 
remote call to the NCBI with the taxonID ?

Thanks for your help,

Morgane.

Morgane THOMAS-CHOLLIER wrote:

> 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

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