This one should be fixed in CVS now. Typo on my behalf - I put in code
to make it work with both 87+ and pre-87 version of EMBL, then got the
regexes the wrong way round!!
Could you send the full stacktrace for the INSDseq format problem you're
having? (The one where you say you've tracked it down to the qualifier
value being missing). I can't see anything wrong there, so I need the
stacktrace in order to know which exact sequence of events is throwing
the exception.
cheers,
Richard
On Fri, 2006-06-02 at 13:04 -0400, Seth Johnson wrote:
> Hi Richard,
>
> I made sure I have the latest source code from CVS compiled
> (EMBLFormat.java & GenbankFormat.java are from 05/24/06). I'm happy
> to report that GenBank issue is solved!!!!
> As far as EMBL parsing, I apologize for not providing the stack dump
> for ISSUE #1. Here's the dump of the exception:
> --------------------------------------------------------
> org.biojava.bio.BioException: Could not read sequence
> at
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112)
> at exonhit.parsers.GenBankParser.main(GenBankParser.java:359)
> Caused by: java.lang.NumberFormatException: null
> at java.lang.Integer.parseInt(Integer.java:415)
> at java.lang.Integer.parseInt(Integer.java:497)
> at
> org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:299)
> at
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109)
> ... 1 more
> Java Result: -1
> -------------------------------------------------------
> Here, again, is the code that I'm using to to parse:
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> BufferedReader gbBR = null;
> try {
> gbBR = new BufferedReader(new
> FileReader("C:\\Download\\ASN2BSML\\seth_06_02.emb"));
> } catch (FileNotFoundException fnfe) {
> fnfe.printStackTrace();
> System.exit(-1);
> }
> Namespace gbNspace = (Namespace)
> RichObjectFactory.getObject(SimpleNamespace.class, new
> Object[]{"gbSpace"} );
> RichSequenceIterator gbSeqs =
> RichSequence.IOTools.readEMBLDNA(gbBR,gbNspace);
> while (gbSeqs.hasNext()) {
> try {
> RichSequence rs = gbSeqs.nextRichSequence();
> NCBITaxon myTaxon = rs.getTaxon();
> }catch (BioException be){
> be.printStackTrace();
> System.exit(-1);
> }
> }
> ~~~~~~~~~~~~~~~~~~~~~~~~~
> And here's the EMBL file that I'm trying to parse:
> +++++++++++++++++++++++++
> ID DQ472184 standard; DNA; INV; 546 BP.
> XX
> AC DQ472184;
> XX
> SV DQ472184.1
> DT 15-MAY-2006
> XX
> DE Trypanosoma cruzi strain CL Brener actin-related protein 3 (ARC21) gene,
> DE complete cds.
> XX
> KW .
> XX
> OS Trypanosoma cruzi strain CL Brener
> OC Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma;
> OC Schizotrypanum.
> XX
> RN [1]
> RP 1-546
> RA De Melo L.D.B.;
> RT "Actin of Trypanosoma cruzi: ubiquitous actin-binding proteins";
> RL Unpublished.
> XX
> RN [2]
> RP 1-546
> RA De Melo L.D.B.;
> RT ;
> RL Submitted (03-APR-2006) to the EMBL/GenBank/DDBJ databases.
> RL Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio
> RL de Janeiro, Cidade Universitaria, CCS, Bl.G, Sl.G157, Rio de Janeiro, RJ
> RL 21949-900, Brazil
> XX
> FH Key Location/Qualifiers
> FH
> FT source 1..546
> FT /organism="Trypanosoma cruzi strain CL Brener"
> FT /mol_type="genomic DNA"
> FT /strain="CL Brener"
> FT /db_xref="taxon:353153"
> FT gene <1..>546
> FT /gene="ARC21"
> FT /note="TcARC21"
> FT mRNA <1..>546
> FT /gene="ARC21"
> FT /product="actin-related protein 3"
> FT CDS 1..546
> FT /gene="ARC21"
> FT /note="actin-binding protein; ARPC3 21 kDa; putative
> FT member of Arp2/3 complex"
> FT /codon_start=1
> FT /product="actin-related protein 3"
> FT /protein_id="ABF13401.1"
> FT /db_xref="GI:93360014"
> FT /translation="MHSRWNGYEESSLLGCGVYPLRRTSRLTPPGPAPRMDEMIEEG
> FT EEEPQDIVDEAFYFFKPHMFFRNFPIKGAGDRVILYLTMYLHECLKKIVQLKREEAH
> FT SVLLNYATMPFASPGEKDFPFNAFFPAGNEEEQEKWREYAKQLRLEANARLIEKVFL
> FT FPEKDGTGNKFWMAFAKRPFLASS"
> atgcacagca ggtggaatgg gtatgaagaa agtagtcttt tgggctgcgg tgtttatccg
> 60
> cttcgccgca cgtcacggct cactccaccc ggccctgcac cgcggatgga tgaaatgatt
> 120
> gaggagggcg aagaggagcc acaagacatt gttgacgagg cattttactt ttttaagccc
> 180
> cacatgtttt ttcgtaattt tcccattaag ggtgctggtg atcgtgtcat tctgtacttg
> 240
> acgatgtacc ttcatgagtg tttgaagaaa attgtccagt tgaagcgtga agaggcccat
> 300
> tctgtgcttc ttaactacgc tacgatgccg tttgcatcac caggggaaaa ggactttccg
> 360
> tttaacgcgt ttttccctgc tgggaatgag gaggaacaag aaaaatggcg agagtatgca
> 420
> aaacagcttc gattggaggc caacgcacgt ctcattgaga aggtttttct ttttccagag
> 480
> aaggacggca ccggaaacaa gttctggatg gcgtttgcga agaggccttt cttggcttct
> 540
> agttag
> 546
> //
> ID DQ472185 standard; DNA; INV; 543 BP.
> XX
> AC DQ472185;
> XX
> SV DQ472185.1
> DT 15-MAY-2006
> XX
> DE Trypanosoma cruzi strain CL Brener actin-related protein 4 (ARC20) gene,
> DE complete cds.
> XX
> KW .
> XX
> OS Trypanosoma cruzi strain CL Brener
> OC Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma;
> OC Schizotrypanum.
> XX
> RN [1]
> RP 1-543
> RA De Melo L.D.B.;
> RT "Actin of Trypanosoma cruzi: ubiquitous actin-binding proteins";
> RL Unpublished.
> XX
> RN [2]
> RP 1-543
> RA De Melo L.D.B.;
> RT ;
> RL Submitted (03-APR-2006) to the EMBL/GenBank/DDBJ databases.
> RL Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio
> RL de Janeiro, Cidade Universitaria, CCS, Bl.G, Sl.G157, Rio de Janeiro, RJ
> RL 21949-900, Brazil
> XX
> FH Key Location/Qualifiers
> FH
> FT source 1..543
> FT /organism="Trypanosoma cruzi strain CL Brener"
> FT /mol_type="genomic DNA"
> FT /strain="CL Brener"
> FT /db_xref="taxon:353153"
> FT gene <1..>543
> FT /gene="ARC20"
> FT /note="TcARC20"
> FT mRNA <1..>543
> FT /gene="ARC20"
> FT /product="actin-related protein 4"
> FT CDS 1..543
> FT /gene="ARC20"
> FT /note="actin-binding protein; ARPC4 20 kDa; putative
> FT member of Arp2/3 complex"
> FT /codon_start=1
> FT /product="actin-related protein 4"
> FT /protein_id="ABF13402.1"
> FT /db_xref="GI:93360016"
> FT /translation="MATAYLPYYDCIKCTLHAALCIGNYPSCTVERHNKPEVEVADH
> FT LENNGEIKVQDFLLNPIRIVRSEQESCLIEPSINSTRISVSFLKSDAIAEIIARKYV
> FT GFLAQRAKQFHILRKKPIPGYDISFLISHEEVETMHRNRIIQFIITFLMDIDADIAA
> FT MKLNVNQRARRAAMEFFLALNFT"
> atggcaaccg cctatttgcc ttactacgac tgcatcaagt gcacgttgca cgcggctttg
> 60
> tgcatcggga attatccttc atgtaccgtg gagcgtcata ataaaccaga agttgaggtt
> 120
> gcagaccatc tggagaataa tggtgaaata aaagtacaag atttccttct taaccccata
> 180
> cgcattgtgc gttcagaaca ggaaagttgt cttattgaac ctagtataaa cagcacacgc
> 240
> atatctgtat cgtttctcaa gagcgacgct attgcagaga ttattgcccg aaagtacgtt
> 300
> ggatttttag ctcagcgagc caaacagttt cacatcttga gaaaaaagcc tattccggga
> 360
> tatgatataa gttttttgat ttctcacgag gaagtagaaa caatgcatag gaataggatt
> 420
> attcaattta taattacttt cttgatggat attgatgctg acattgctgc aatgaagttg
> 480
> aatgtgaatc aacgtgcacg tcgagcagcg atggaattct ttcttgcatt gaatttcaca
> 540
> tga
> 543
> //
> +++++++++++++++++++++++++++++++++
>
> It looks to me like there's some kind of problem with parsing the
> sequence version number. I even tried the sequence from test directory
> (AY069118.em) with same outcome.
>
> Regards,
>
> Seth
>
> On 6/2/06, Richard Holland <[EMAIL PROTECTED]> wrote:
> > Hi Seth.
> >
> > Your second point, about the authors string not being read correctly in
> > Genbank format, has been fixed (or should have been if I got the code
> > right!). Could you check the latest version of biojava-live out of CVS
> > and give it another go? Basically the parser did not recognise the
> > CONSRTM tag, as it is not mentioned in the sample record provided by
> > NCBI, which is what I based the parser on.
> >
> > I've set it up now so that it reads the CONSRTM tag, but the value is
> > merged with the authors tag with (consortium) appended. There will still
> > be problems if the consortium value has commas in it - not sure how to
> > fix this yet.
> >
> > Your first point is harder to solve because you did not provide a
> > complete stack trace for the exceptions you are getting. The complete
> > stack trace would enable me to identify exactly where things are going
> > wrong and give me a better chance of fixing them. Could you send the
> > stack trace, and I'll see what I can do.
> >
> > cheers,
> > Richard
> >
> >
> > On Thu, 2006-06-01 at 18:03 -0400, Seth Johnson wrote:
> > > Hi All,
> > >
> > > I'm a newbie to the whole BioJava(X) API and was hoping to get some
> > > clarification on several issues that I'm having.
> > > I am developing a parser that would take as input "NCBI Incremental
> > > ASN.1 Sequence Updates to Genbank" files (
> > > ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily-nc ) , gunzip them, and use the
> > > ASN2GB converter (
> > > ftp://ftp.ncbi.nih.gov/asn1-converters/by_program/asn2gb ) to convert
> > > resulting sequences to a format parsable by BioJava(X) (
> > > http://www.penguin-soft.com/penguin/man/1/asn2gb.html ). This is where
> > > my problems start.
> > >
> > > ISSUE 1:
> > > I've tried to parse all of the formats that ASN2GB outputs ( GenBank
> > > (default) , EMBL, nucleotide GBSet (XML), nucleotide INSDSet (XML),
> > > tiny seq (XML) ) using either BioJava or BioJavaX API. Only GenBank
> > > format is recognized by the
> > > "RichSequence.IOTools.readGenbankDNA(inBuf,gbNspace)" function with
> > > some exceptions that I'll describe in issue #2. This is the code that
> > > I'm using to parse, for example, the EMBL output:
> > >
> > > BufferedReader inBuf = new BufferedReader(new
> > > FileReader("embl_output.emb"));
> > > Namespace gbNspace = (Namespace)
> > > RichObjectFactory.getObject(SimpleNamespace.class, new
> > > Object[]{"gbSpace"} );
> > > RichSequenceIterator gbSeqs =
> > > RichSequence.IOTools.readEMBLDNA(inBuf,gbNspace);
> > > while (gbSeqs.hasNext()) {
> > > try {
> > > RichSequence rs = gbSeqs.nextRichSequence();
> > > // Further processing or RichSequence object from here
> > >
> > > } catch (BioException be){
> > > be.printStackTrace();
> > > }
> > > }
> > >
> > > The multi-sequence EMBL file looks like this:
> > > ---------------------------------------------------------------------------------
> > > ID DQ472184 standard; DNA; INV; 546 BP.
> > > XX
> > > AC DQ472184;
> > > XX
> > > SV DQ472184.1
> > > DT 15-MAY-2006
> > > XX
> > > DE Trypanosoma cruzi strain CL Brener actin-related protein 3 (ARC21)
> > > gene,
> > > DE complete cds.
> > > XX
> > > KW .
> > > XX
> > > OS Trypanosoma cruzi strain CL Brener
> > > OC Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma;
> > > OC Schizotrypanum.
> > > XX
> > > RN [1]
> > > RP 1-546
> > > RA De Melo L.D.B.;
> > > RT "Actin of Trypanosoma cruzi: ubiquitous actin-binding proteins";
> > > RL Unpublished.
> > > XX
> > > RN [2]
> > > RP 1-546
> > > RA De Melo L.D.B.;
> > > RT ;
> > > RL Submitted (03-APR-2006) to the EMBL/GenBank/DDBJ databases.
> > > RL Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do
> > > Rio
> > > RL de Janeiro, Cidade Universitaria, CCS, Bl.G, Sl.G157, Rio de
> > > Janeiro, RJ
> > > RL 21949-900, Brazil
> > > XX
> > > FH Key Location/Qualifiers
> > > FH
> > > FT source 1..546
> > > FT /organism="Trypanosoma cruzi strain CL Brener"
> > > FT /mol_type="genomic DNA"
> > > FT /strain="CL Brener"
> > > FT /db_xref="taxon:353153"
> > > FT gene <1..>546
> > > FT /gene="ARC21"
> > > FT /note="TcARC21"
> > > FT mRNA <1..>546
> > > FT /gene="ARC21"
> > > FT /product="actin-related protein 3"
> > > FT CDS 1..546
> > > FT /gene="ARC21"
> > > FT /note="actin-binding protein; ARPC3 21 kDa; putative
> > > FT member of Arp2/3 complex"
> > > FT /codon_start=1
> > > FT /product="actin-related protein 3"
> > > FT /protein_id="ABF13401.1"
> > > FT /db_xref="GI:93360014"
> > > FT
> > > /translation="MHSRWNGYEESSLLGCGVYPLRRTSRLTPPGPAPRMDEMIEEG
> > > FT
> > > EEEPQDIVDEAFYFFKPHMFFRNFPIKGAGDRVILYLTMYLHECLKKIVQLKREEAH
> > > FT
> > > SVLLNYATMPFASPGEKDFPFNAFFPAGNEEEQEKWREYAKQLRLEANARLIEKVFL
> > > FT FPEKDGTGNKFWMAFAKRPFLASS"
> > > atgcacagca ggtggaatgg gtatgaagaa agtagtcttt tgggctgcgg tgtttatccg
> > > 60
> > > cttcgccgca cgtcacggct cactccaccc ggccctgcac cgcggatgga tgaaatgatt
> > > 120
> > > gaggagggcg aagaggagcc acaagacatt gttgacgagg cattttactt ttttaagccc
> > > 180
> > > cacatgtttt ttcgtaattt tcccattaag ggtgctggtg atcgtgtcat tctgtacttg
> > > 240
> > > acgatgtacc ttcatgagtg tttgaagaaa attgtccagt tgaagcgtga agaggcccat
> > > 300
> > > tctgtgcttc ttaactacgc tacgatgccg tttgcatcac caggggaaaa ggactttccg
> > > 360
> > > tttaacgcgt ttttccctgc tgggaatgag gaggaacaag aaaaatggcg agagtatgca
> > > 420
> > > aaacagcttc gattggaggc caacgcacgt ctcattgaga aggtttttct ttttccagag
> > > 480
> > > aaggacggca ccggaaacaa gttctggatg gcgtttgcga agaggccttt cttggcttct
> > > 540
> > > agttag
> > > 546
> > > //
> > > ID DQ472185 standard; DNA; INV; 543 BP.
> > > XX
> > > AC DQ472185;
> > > XX
> > > SV DQ472185.1
> > > DT 15-MAY-2006
> > > XX
> > > DE Trypanosoma cruzi strain CL Brener actin-related protein 4 (ARC20)
> > > gene,
> > > DE complete cds.
> > > XX
> > > KW .
> > > XX
> > > OS Trypanosoma cruzi strain CL Brener
> > > OC Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma;
> > > OC Schizotrypanum.
> > > XX
> > > RN [1]
> > > RP 1-543
> > > RA De Melo L.D.B.;
> > > RT "Actin of Trypanosoma cruzi: ubiquitous actin-binding proteins";
> > > RL Unpublished.
> > > XX
> > > RN [2]
> > > RP 1-543
> > > RA De Melo L.D.B.;
> > > RT ;
> > > RL Submitted (03-APR-2006) to the EMBL/GenBank/DDBJ databases.
> > > RL Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do
> > > Rio
> > > RL de Janeiro, Cidade Universitaria, CCS, Bl.G, Sl.G157, Rio de
> > > Janeiro, RJ
> > > RL 21949-900, Brazil
> > > XX
> > > FH Key Location/Qualifiers
> > > FH
> > > FT source 1..543
> > > FT /organism="Trypanosoma cruzi strain CL Brener"
> > > FT /mol_type="genomic DNA"
> > > FT /strain="CL Brener"
> > > FT /db_xref="taxon:353153"
> > > FT gene <1..>543
> > > FT /gene="ARC20"
> > > FT /note="TcARC20"
> > > FT mRNA <1..>543
> > > FT /gene="ARC20"
> > > FT /product="actin-related protein 4"
> > > FT CDS 1..543
> > > FT /gene="ARC20"
> > > FT /note="actin-binding protein; ARPC4 20 kDa; putative
> > > FT member of Arp2/3 complex"
> > > FT /codon_start=1
> > > FT /product="actin-related protein 4"
> > > FT /protein_id="ABF13402.1"
> > > FT /db_xref="GI:93360016"
> > > FT
> > > /translation="MATAYLPYYDCIKCTLHAALCIGNYPSCTVERHNKPEVEVADH
> > > FT
> > > LENNGEIKVQDFLLNPIRIVRSEQESCLIEPSINSTRISVSFLKSDAIAEIIARKYV
> > > FT
> > > GFLAQRAKQFHILRKKPIPGYDISFLISHEEVETMHRNRIIQFIITFLMDIDADIAA
> > > FT MKLNVNQRARRAAMEFFLALNFT"
> > > atggcaaccg cctatttgcc ttactacgac tgcatcaagt gcacgttgca cgcggctttg
> > > 60
> > > tgcatcggga attatccttc atgtaccgtg gagcgtcata ataaaccaga agttgaggtt
> > > 120
> > > gcagaccatc tggagaataa tggtgaaata aaagtacaag atttccttct taaccccata
> > > 180
> > > cgcattgtgc gttcagaaca ggaaagttgt cttattgaac ctagtataaa cagcacacgc
> > > 240
> > > atatctgtat cgtttctcaa gagcgacgct attgcagaga ttattgcccg aaagtacgtt
> > > 300
> > > ggatttttag ctcagcgagc caaacagttt cacatcttga gaaaaaagcc tattccggga
> > > 360
> > > tatgatataa gttttttgat ttctcacgag gaagtagaaa caatgcatag gaataggatt
> > > 420
> > > attcaattta taattacttt cttgatggat attgatgctg acattgctgc aatgaagttg
> > > 480
> > > aatgtgaatc aacgtgcacg tcgagcagcg atggaattct ttcttgcatt gaatttcaca
> > > 540
> > > tga
> > > 543
> > > //
> > > -----------------------------------------------------------------------
> > > I get an exception message "Could Not Read Sequence". Same thing
> > > happens if I use the readINSDSetDNA reader instead of readEMBLDNA one
> > > with the following INSDset file (beginning of the file):
> > >
> > > <?xml version="1.0"?>
> > > <!DOCTYPE INSDSeq PUBLIC "-//NCBI//INSD INSDSeq/EN" "INSD_INSDSeq.dtd">
> > > <INSDSeq>
> > > <INSDSeq_locus>DQ022078</INSDSeq_locus>
> > > <INSDSeq_length>16729</INSDSeq_length>
> > > <INSDSeq_moltype>DNA</INSDSeq_moltype>
> > > <INSDSeq_topology>linear</INSDSeq_topology>
> > > <INSDSeq_division>ENV</INSDSeq_division>
> > > <INSDSeq_update-date>15-MAY-2006</INSDSeq_update-date>
> > > <INSDSeq_create-date>15-MAY-2006</INSDSeq_create-date>
> > > <INSDSeq_definition>Uncultured bacterium WWRS-2005 putative
> > > aminoglycoside phosphotransferase (a3.001), putative oxidoreductase
> > > (a3.002), putative oxidoreductase (a3.003), putative beta-lactamase
> > > class C (estA3), putative permease (a3.005), putative transmembrane
> > > signal peptide (a3.006), thiol-disulfide isomerase (a3.007), histone
> > > acetyltransferase HPA2 (a3.008), putative enzyme (a3.009), putative
> > > asparaginase (a3.010), hypothetical protein (a3.011), hypothetical
> > > protein (a3.012), putative membrane protease subunit (a3.013),
> > > putative haloalkane dehalogenase (a3.014), putative transcriptional
> > > regulator (a3.015), putative peptidyl-dipeptidase Dcp (a3.016), and
> > > hypothetical protein (a3.017) genes, complete cds</INSDSeq_definition>
> > > <INSDSeq_primary-accession>DQ022078</INSDSeq_primary-accession>
> > > <INSDSeq_other-seqids>
> > > <INSDSeqid>gb|DQ022078.1|</INSDSeqid>
> > > <INSDSeqid>gi|71842722</INSDSeqid>
> > > </INSDSeq_other-seqids>
> > > <INSDSeq_keywords>
> > > <INSDKeyword>ENV</INSDKeyword>
> > > </INSDSeq_keywords>
> > > <INSDSeq_references>
> > > <INSDReference>
> > > <INSDReference_reference>?</INSDReference_reference>
> > > <INSDReference_position>1..16729</INSDReference_position>
> > > <INSDReference_authors>
> > > <INSDAuthor>Schmeisser,C.</INSDAuthor>
> > > <INSDAuthor>Elend,C.</INSDAuthor>
> > > <INSDAuthor>Streit,W.R.</INSDAuthor>
> > > </INSDReference_authors>
> > > <INSDReference_title>Isolation and biochemical characterization
> > > of two novel metagenome derived esterases</INSDReference_title>
> > > <INSDReference_journal>Appl. Environ. Microbiol. 0:0-0
> > > (2006)</INSDReference_journal>
> > > </INSDReference>
> > > <INSDReference>
> > > <INSDReference_reference>?</INSDReference_reference>
> > > <INSDReference_position>1..16729</INSDReference_position>
> > > <INSDReference_authors>
> > > <INSDAuthor>Schmeisser,C.</INSDAuthor>
> > > <INSDAuthor>Elend,C.</INSDAuthor>
> > > <INSDAuthor>Streit,W.R.</INSDAuthor>
> > > </INSDReference_authors>
> > > <INSDReference_journal>Submitted (29-APR-2005) to the
> > > EMBL/GenBank/DDBJ databases. Molekulare Enzymtechnologie, University
> > > Duisburg-Essen, Lotharstrasse 1, Duisburg D-47057,
> > > Germany</INSDReference_journal>
> > > </INSDReference>
> > > </INSDSeq_references>
> > >
> > > So my question is wether the ASN2GB produces output that's
> > > incompatible with BioJava parsers or is there a problem with the
> > > sequence themselves or the problems with the majority of parsers???
> > > Could it be that I'm using the API wrongly for the above formats,
> > > although GenBank parser works as advertised with some exceptions
> > > below:
> > >
> > > ISSUE #2:
> > > When I try to parse GenBank files using the following code:
> > >
> > > BufferedReader inBuf = new BufferedReader(new
> > > FileReader("genbank_output.gb"));
> > > Namespace gbNspace = (Namespace)
> > > RichObjectFactory.getObject(SimpleNamespace.class, new
> > > Object[]{"gbSpace"} );
> > > RichSequenceIterator gbSeqs =
> > > RichSequence.IOTools.readGenbankDNA(inBuf,gbNspace);
> > > while (gbSeqs.hasNext()) {
> > > try {
> > > RichSequence rs = gbSeqs.nextRichSequence();
> > > // Further processing or RichSequence object from here
> > >
> > > } catch (BioException be){
> > > be.printStackTrace();
> > > }
> > > }
> > >
> > > Genbank file in question:
> > >
> > > LOCUS BC074905 838 bp mRNA linear PRI
> > > 15-APR-2006
> > > DEFINITION Homo sapiens kallikrein 14, mRNA (cDNA clone MGC:104038
> > > IMAGE:30915482), complete cds.
> > > ACCESSION BC074905
> > > VERSION BC074905.2 GI:50959825
> > > KEYWORDS MGC.
> > > SOURCE Homo sapiens (human)
> > > ORGANISM Homo sapiens
> > > Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
> > > Euteleostomi;
> > > Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
> > > Catarrhini; Hominidae; Homo.
> > > REFERENCE 1 (bases 1 to 838)
> > > AUTHORS Strausberg,R.L., Feingold,E.A., Grouse,L.H., Derge,J.G.,
> > > Klausner,R.D., Collins,F.S., Wagner,L., Shenmen,C.M.,
> > > Schuler,G.D.,
> > > Altschul,S.F., Zeeberg,B., Buetow,K.H., Schaefer,C.F.,
> > > Bhat,N.K.,
> > > Hopkins,R.F., Jordan,H., Moore,T., Max,S.I., Wang,J.,
> > > Hsieh,F.,
> > > Diatchenko,L., Marusina,K., Farmer,A.A., Rubin,G.M., Hong,L.,
> > > Stapleton,M., Soares,M.B., Bonaldo,M.F., Casavant,T.L.,
> > > Scheetz,T.E., Brownstein,M.J., Usdin,T.B., Toshiyuki,S.,
> > > Carninci,P., Prange,C., Raha,S.S., Loquellano,N.A.,
> > > Peters,G.J.,
> > > Abramson,R.D., Mullahy,S.J., Bosak,S.A., McEwan,P.J.,
> > > McKernan,K.J., Malek,J.A., Gunaratne,P.H., Richards,S.,
> > > Worley,K.C., Hale,S., Garcia,A.M., Gay,L.J., Hulyk,S.W.,
> > > Villalon,D.K., Muzny,D.M., Sodergren,E.J., Lu,X., Gibbs,R.A.,
> > > Fahey,J., Helton,E., Ketteman,M., Madan,A., Rodrigues,S.,
> > > Sanchez,A., Whiting,M., Madan,A., Young,A.C., Shevchenko,Y.,
> > > Bouffard,G.G., Blakesley,R.W., Touchman,J.W., Green,E.D.,
> > > Dickson,M.C., Rodriguez,A.C., Grimwood,J., Schmutz,J.,
> > > Myers,R.M.,
> > > Butterfield,Y.S., Krzywinski,M.I., Skalska,U., Smailus,D.E.,
> > > Schnerch,A., Schein,J.E., Jones,S.J. and Marra,M.A.
> > > CONSRTM Mammalian Gene Collection Program Team
> > > TITLE Generation and initial analysis of more than 15,000
> > > full-length
> > > human and mouse cDNA sequences
> > > JOURNAL Proc. Natl. Acad. Sci. U.S.A. 99 (26), 16899-16903 (2002)
> > > PUBMED 12477932
> > > REFERENCE 2 (bases 1 to 838)
> > > CONSRTM NIH MGC Project
> > > TITLE Direct Submission
> > > JOURNAL Submitted (25-JUN-2004) National Institutes of Health,
> > > Mammalian
> > > Gene Collection (MGC), Bethesda, MD 20892-2590, USA
> > > REMARK NIH-MGC Project URL: http://mgc.nci.nih.gov
> > > COMMENT On Aug 4, 2004 this sequence version replaced gi:49901832.
> > > Contact: MGC help desk
> > > Email: [EMAIL PROTECTED]
> > > Tissue Procurement: Genome Sequence Centre, British Columbia
> > > Cancer
> > > Center
> > > cDNA Library Preparation: British Columbia Cancer Research
> > > Center
> > > cDNA Library Arrayed by: The I.M.A.G.E. Consortium (LLNL)
> > > DNA Sequencing by: Genome Sequence Centre,
> > > BC Cancer Agency, Vancouver, BC, Canada
> > > [EMAIL PROTECTED]
> > > Martin Hirst, Thomas Zeng, Ryan Morin, Michelle Moksa, Johnson
> > > Pang, Diana Mah, Jing Wang, Kieth Fichter, Eric Chuah, Allen
> > > Delaney, Rob Kirkpatrick, Agnes Baross, Sarah Barber, Mabel
> > > Brown-John, Steve S. Chand, William Chow, Ryan Babakaiff, Dave
> > > Wong, Corey Matsuo, Jaclyn Beland, Susan Gibson, Luis delRio,
> > > Ruth
> > > Featherstone, Malachi Griffith, Obi Griffith, Ran Guin, Nancy
> > > Liao,
> > > Kim MacDonald, Mike R. Mayo, Josh Moran, Diana Palmquist, JR
> > > Santos, Duane Smailus, Jeff Stott, Miranda Tsai, George Yang,
> > > Jacquie Schein, Asim Siddiqui,Steven Jones, Rob Holt, Marco
> > > Marra.
> > >
> > > Clone distribution: MGC clone distribution information can be
> > > found
> > > through the I.M.A.G.E. Consortium/LLNL at:
> > > http://image.llnl.gov
> > > Series: IRBU Plate: 4 Row: C Column: 3.
> > >
> > > Differences found between this sequence and the human
> > > reference
> > > genome (build 36) are described in misc_difference features
> > > below.
> > > FEATURES Location/Qualifiers
> > > source 1..838
> > > /organism="Homo sapiens"
> > > /mol_type="mRNA"
> > > /db_xref="taxon:9606"
> > > /clone="MGC:104038 IMAGE:30915482"
> > > /tissue_type="Lung, PCR rescued clones"
> > > /clone_lib="NIH_MGC_273"
> > > /lab_host="DH10B"
> > > /note="Vector: pCR4 Topo TA with reversed insert"
> > > gene 1..838
> > > /gene="KLK14"
> > > /note="synonym: KLK-L6"
> > > /db_xref="GeneID:43847"
> > > /db_xref="HGNC:6362"
> > > /db_xref="IMGT/GENE-DB:6362"
> > > /db_xref="MIM:606135"
> > > CDS 49..804
> > > /gene="KLK14"
> > > /codon_start=1
> > > /product="KLK14 protein"
> > > /protein_id="AAH74905.1"
> > > /db_xref="GI:50959826"
> > > /db_xref="GeneID:43847"
> > > /db_xref="HGNC:6362"
> > > /db_xref="IMGT/GENE-DB:6362"
> > > /db_xref="MIM:606135"
> > >
> > > /translation="MFLLLTALQVLAIAMTRSQEDENKIIGGYTCTRSSQPWQAALLA
> > >
> > > GPRRRFLCGGALLSGQWVITAAHCGRPILQVALGKHNLRRWEATQQVLRVVRQVTHPN
> > >
> > > YNSRTHDNDLMLLQLQQPARIGRAVRPIEVTQACASPGTSCRVSGWGTISSPIARYPA
> > >
> > > SLQCVNINISPDEVCQKAYPRTITPGMVCAGVPQGGKDSCQGDSGGPLVCRGQLQGLV
> > > SWGMERCALPGYPGVYTNLCKYRSWIEETMRDK"
> > > misc_difference 98
> > > /gene="KLK14"
> > > /note="'G' in cDNA is 'A' in the human genome; amino
> > > acid
> > > difference: 'R' in cDNA, 'Q' in the human genome."
> > > misc_difference 133
> > > /gene="KLK14"
> > > /note="'T' in cDNA is 'C' in the human genome; amino
> > > acid
> > > difference: 'Y' in cDNA, 'H' in the human genome."
> > > ORIGIN
> > > 1 atgtccctga gggtcttggg ctctgggacc tggccctcag cccctaaaat
> > > gttcctcctg
> > > 61 ctgacagcac ttcaagtcct ggctatagcc atgacacgga gccaagagga
> > > tgagaacaag
> > > 121 ataattggtg gctatacgtg cacccggagc tcccagccgt ggcaggcggc
> > > cctgctggcg
> > > 181 ggtcccaggc gccgcttcct ctgcggaggc gccctgcttt caggccagtg
> > > ggtcatcact
> > > 241 gctgctcact gcggccgccc gatccttcag gttgccctgg gcaagcacaa
> > > cctgaggagg
> > > 301 tgggaggcca cccagcaggt gctgcgcgtg gttcgtcagg tgacgcaccc
> > > caactacaac
> > > 361 tcccggaccc acgacaacga cctcatgctg ctgcagctac agcagcccgc
> > > acggatcggg
> > > 421 agggcagtca ggcccattga ggtcacccag gcctgtgcca gccccgggac
> > > ctcctgccga
> > > 481 gtgtcaggct ggggaactat atccagcccc atcgccaggt accccgcctc
> > > tctgcaatgc
> > > 541 gtgaacatca acatctcccc ggatgaggtg tgccagaagg cctatcctag
> > > aaccatcacg
> > > 601 cctggcatgg tctgtgcagg agttccccag ggcgggaagg actcttgtca
> > > gggtgactct
> > > 661 gggggacccc tggtgtgcag aggacagctc cagggcctcg tgtcttgggg
> > > aatggagcgc
> > > 721 tgcgccctgc ctggctaccc cggtgtctac accaacctgt gcaagtacag
> > > aagctggatt
> > > 781 gaggaaacga tgcgggacaa atgatggtct tcacggtggg atggacctcg tcagctgc
> > > //
> > >
> > > I get the following exception:
> > >
> > > java.lang.IllegalArgumentException: Authors string cannot be null
> > > org.biojava.bio.BioException: Could not read sequence
> > > at
> > > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112)
> > > at
> > > exonhit.parsers.GenBankParser.getSequences(GenBankParser.java:107)
> > > at
> > > exonhit.parsers.GenBankParser.runGBparser(GenBankParser.java:258)
> > > at exonhit.parsers.GenBankParser.main(GenBankParser.java:341)
> > > Caused by: java.lang.IllegalArgumentException: Authors string cannot be
> > > null
> > > at
> > > org.biojavax.DocRefAuthor$Tools.parseAuthorString(DocRefAuthor.java:76)
> > > at
> > > org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:356)
> > > at
> > > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109)
> > >
> > > -----------------------------------------------------------------------
> > >
> > > I'm trying to see what could be the problem with this particular
> > > sequence. Looks to me like the AUTHORS portion is not getting parsed
> > > correctly. Any ideas would be greatly appreciated!
> > >
> > --
> > Richard Holland (BioMart Team)
> > EMBL-EBI
> > Wellcome Trust Genome Campus
> > Hinxton
> > Cambridge CB10 1SD
> > UNITED KINGDOM
> > Tel: +44-(0)1223-494416
> >
> >
>
>
--
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416
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