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http://lists.open-bio.org/mailman/listinfo/biojava-l cheers, Richard On Tue, 2006-06-06 at 11:16 -0400, Luba wrote: > Hey, guys, > Do you know how to unsubscribe from the list? > > Thanks. > > ----- Original Message ----- > From: "Seth Johnson" <[EMAIL PROTECTED]> > To: "Richard Holland" <[EMAIL PROTECTED]> > Cc: <[email protected]> > Sent: Tuesday, June 06, 2006 10:34 AM > Subject: Re: [Biojava-l] Parsing INSDseq Sequences (1.3 & 1.4) > > > >I think it would be best to wait for the 'official response'. I could > > only locate the general changes detailed here: > > > > http://www.bio.net/bionet/mm/genbankb/2005-December/000233.html > > > > As far as the solution to the ever changing formats I just don't see > > an elegant way. :( The only things that comes to mind is creating > > separate format "INSDseq14Format.java" and build new readers & writers > > on top of that. > > > > #1: And on that note I wanted to ask about differences between Genbank > > & INSDseq parsers and a ways to retrieve certain values. The tutorial > > states that those two formats are essentialy mirror images of each > > other with the latter being an XML. When parsing Genbank files > > "rs.getIdentifier()" retrieves the GI number, however, when the same > > function is used on RichSequence obtained by parsing INSDseq format, I > > get a 'null' value. Moreover, I could not even locate that number > > during debugging in the structure of RichSequence object. Is there a > > bug or GI number should be obtained differently??? > > > > #2: Also, what is the best way to obtain "mol_type" value from > > RichSequence object??? The tutorial states that it's > > "getNoteSet(Terms.getMolTypeTerm())". I guess it' either a simplified > > explanation or something has changed since .getNoteSet() does not take > > any parameters. I used > > "rs.getAnnotation().asMap().get(Terms.getMolTypeTerm())" and was > > wondering if that's how it was intended to be retrieved. > > > > As always, below is the INSDseq file I tried to parse: > > ================================ > > <?xml version="1.0"?> > > <!DOCTYPE INSDSet PUBLIC "-//NCBI//INSD INSDSeq/EN" > > "http://www.ncbi.nlm.nih.gov/dtd/INSD_INSDSeq.dtd";> > > <INSDSet> > > <INSDSeq> > > <INSDSeq_locus>AY069118</INSDSeq_locus> > > <INSDSeq_length>1502</INSDSeq_length> > > <INSDSeq_strandedness>single</INSDSeq_strandedness> > > <INSDSeq_moltype>mRNA</INSDSeq_moltype> > > <INSDSeq_topology>linear</INSDSeq_topology> > > <INSDSeq_division>INV</INSDSeq_division> > > <INSDSeq_update-date>17-DEC-2001</INSDSeq_update-date> > > <INSDSeq_create-date>15-DEC-2001</INSDSeq_create-date> > > <INSDSeq_definition>Drosophila melanogaster GH13089 full length > > cDNA</INSDSeq_definition> > > <INSDSeq_primary-accession>AY069118</INSDSeq_primary-accession> > > <INSDSeq_accession-version>AY069118.1</INSDSeq_accession-version> > > <INSDSeq_other-seqids> > > <INSDSeqid>gb|AY069118.1|</INSDSeqid> > > <INSDSeqid>gi|17861571</INSDSeqid> > > </INSDSeq_other-seqids> > > <INSDSeq_keywords> > > <INSDKeyword>FLI_CDNA</INSDKeyword> > > </INSDSeq_keywords> > > <INSDSeq_source>Drosophila melanogaster (fruit fly)</INSDSeq_source> > > <INSDSeq_organism>Drosophila melanogaster</INSDSeq_organism> > > <INSDSeq_taxonomy>Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; > > Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; > > Ephydroidea; Drosophilidae; Drosophila</INSDSeq_taxonomy> > > <INSDSeq_references> > > <INSDReference> > > <INSDReference_reference>1 (bases 1 to > > 1502)</INSDReference_reference> > > <INSDReference_position>1..1502</INSDReference_position> > > <INSDReference_authors> > > <INSDAuthor>Stapleton,M.</INSDAuthor> > > <INSDAuthor>Brokstein,P.</INSDAuthor> > > <INSDAuthor>Hong,L.</INSDAuthor> > > <INSDAuthor>Agbayani,A.</INSDAuthor> > > <INSDAuthor>Carlson,J.</INSDAuthor> > > <INSDAuthor>Champe,M.</INSDAuthor> > > <INSDAuthor>Chavez,C.</INSDAuthor> > > <INSDAuthor>Dorsett,V.</INSDAuthor> > > <INSDAuthor>Farfan,D.</INSDAuthor> > > <INSDAuthor>Frise,E.</INSDAuthor> > > <INSDAuthor>George,R.</INSDAuthor> > > <INSDAuthor>Gonzalez,M.</INSDAuthor> > > <INSDAuthor>Guarin,H.</INSDAuthor> > > <INSDAuthor>Li,P.</INSDAuthor> > > <INSDAuthor>Liao,G.</INSDAuthor> > > <INSDAuthor>Miranda,A.</INSDAuthor> > > <INSDAuthor>Mungall,C.J.</INSDAuthor> > > <INSDAuthor>Nunoo,J.</INSDAuthor> > > <INSDAuthor>Pacleb,J.</INSDAuthor> > > <INSDAuthor>Paragas,V.</INSDAuthor> > > <INSDAuthor>Park,S.</INSDAuthor> > > <INSDAuthor>Phouanenavong,S.</INSDAuthor> > > <INSDAuthor>Wan,K.</INSDAuthor> > > <INSDAuthor>Yu,C.</INSDAuthor> > > <INSDAuthor>Lewis,S.E.</INSDAuthor> > > <INSDAuthor>Rubin,G.M.</INSDAuthor> > > <INSDAuthor>Celniker,S.</INSDAuthor> > > </INSDReference_authors> > > <INSDReference_title>Direct Submission</INSDReference_title> > > <INSDReference_journal>Submitted (10-DEC-2001) Berkeley > > Drosophila Genome Project, Lawrence Berkeley National Laboratory, One > > Cyclotron Road, Berkeley, CA 94720, USA</INSDReference_journal> > > </INSDReference> > > </INSDSeq_references> > > <INSDSeq_comment>Sequence submitted by: Berkeley Drosophila Genome > > Project Lawrence Berkeley National Laboratory Berkeley, CA 94720 This > > clone was sequenced as part of a high-throughput process to sequence > > clones from Drosophila Gene Collection 1 (Rubin et al., Science 2000). > > The sequence has been subjected to integrity checks for sequence > > accuracy, presence of a polyA tail and contiguity within 100 kb in the > > genome. Thus we believe the sequence to reflect accurately this > > particular cDNA clone. However, there are artifacts associated with > > the generation of cDNA clones that may have not been detected in our > > initial analyses such as internal priming, priming from contaminating > > genomic DNA, retained introns due to reverse transcription of > > unspliced precursor RNAs, and reverse transcriptase errors that result > > in single base changes. For further information about this sequence, > > including its location and relationship to other sequences, please > > visit our Web site (http://fruitfly.berkeley.edu) or send email to > > [EMAIL PROTECTED]</INSDSeq_comment> > > <INSDSeq_feature-table> > > <INSDFeature> > > <INSDFeature_key>source</INSDFeature_key> > > <INSDFeature_location>1..1502</INSDFeature_location> > > <INSDFeature_intervals> > > <INSDInterval> > > <INSDInterval_from>1</INSDInterval_from> > > <INSDInterval_to>1502</INSDInterval_to> > > <INSDInterval_accession>AY069118.1</INSDInterval_accession> > > </INSDInterval> > > </INSDFeature_intervals> > > <INSDFeature_quals> > > <INSDQualifier> > > <INSDQualifier_name>organism</INSDQualifier_name> > > <INSDQualifier_value>Drosophila > > melanogaster</INSDQualifier_value> > > </INSDQualifier> > > <INSDQualifier> > > <INSDQualifier_name>mol_type</INSDQualifier_name> > > <INSDQualifier_value>mRNA</INSDQualifier_value> > > </INSDQualifier> > > <INSDQualifier> > > <INSDQualifier_name>strain</INSDQualifier_name> > > <INSDQualifier_value>y; cn bw sp</INSDQualifier_value> > > </INSDQualifier> > > <INSDQualifier> > > <INSDQualifier_name>db_xref</INSDQualifier_name> > > <INSDQualifier_value>taxon:7227</INSDQualifier_value> > > </INSDQualifier> > > <INSDQualifier> > > <INSDQualifier_name>map</INSDQualifier_name> > > <INSDQualifier_value>39B3-39B3</INSDQualifier_value> > > </INSDQualifier> > > </INSDFeature_quals> > > </INSDFeature> > > <INSDFeature> > > <INSDFeature_key>gene</INSDFeature_key> > > <INSDFeature_location>1..1502</INSDFeature_location> > > <INSDFeature_intervals> > > <INSDInterval> > > <INSDInterval_from>1</INSDInterval_from> > > <INSDInterval_to>1502</INSDInterval_to> > > <INSDInterval_accession>AY069118.1</INSDInterval_accession> > > </INSDInterval> > > </INSDFeature_intervals> > > <INSDFeature_quals> > > <INSDQualifier> > > <INSDQualifier_name>gene</INSDQualifier_name> > > <INSDQualifier_value>E2f2</INSDQualifier_value> > > </INSDQualifier> > > <INSDQualifier> > > <INSDQualifier_name>note</INSDQualifier_name> > > <INSDQualifier_value>alignment with genomic scaffold > > AE003669</INSDQualifier_value> > > </INSDQualifier> > > <INSDQualifier> > > <INSDQualifier_name>db_xref</INSDQualifier_name> > > <INSDQualifier_value>FLYBASE:FBgn0024371</INSDQualifier_value> > > </INSDQualifier> > > </INSDFeature_quals> > > </INSDFeature> > > <INSDFeature> > > <INSDFeature_key>CDS</INSDFeature_key> > > <INSDFeature_location>189..1301</INSDFeature_location> > > <INSDFeature_intervals> > > <INSDInterval> > > <INSDInterval_from>189</INSDInterval_from> > > <INSDInterval_to>1301</INSDInterval_to> > > <INSDInterval_accession>AY069118.1</INSDInterval_accession> > > </INSDInterval> > > </INSDFeature_intervals> > > <INSDFeature_quals> > > <INSDQualifier> > > <INSDQualifier_name>gene</INSDQualifier_name> > > <INSDQualifier_value>E2f2</INSDQualifier_value> > > </INSDQualifier> > > <INSDQualifier> > > <INSDQualifier_name>note</INSDQualifier_name> > > <INSDQualifier_value>Longest ORF</INSDQualifier_value> > > </INSDQualifier> > > <INSDQualifier> > > <INSDQualifier_name>codon_start</INSDQualifier_name> > > <INSDQualifier_value>1</INSDQualifier_value> > > </INSDQualifier> > > <INSDQualifier> > > <INSDQualifier_name>transl_table</INSDQualifier_name> > > <INSDQualifier_value>1</INSDQualifier_value> > > </INSDQualifier> > > <INSDQualifier> > > <INSDQualifier_name>product</INSDQualifier_name> > > <INSDQualifier_value>GH13089p</INSDQualifier_value> > > </INSDQualifier> > > <INSDQualifier> > > <INSDQualifier_name>protein_id</INSDQualifier_name> > > <INSDQualifier_value>AAL39263.1</INSDQualifier_value> > > </INSDQualifier> > > <INSDQualifier> > > <INSDQualifier_name>db_xref</INSDQualifier_name> > > <INSDQualifier_value>GI:17861572</INSDQualifier_value> > > </INSDQualifier> > > <INSDQualifier> > > <INSDQualifier_name>db_xref</INSDQualifier_name> > > <INSDQualifier_value>FLYBASE:FBgn0024371</INSDQualifier_value> > > </INSDQualifier> > > <INSDQualifier> > > <INSDQualifier_name>translation</INSDQualifier_name> > > > > <INSDQualifier_value>MYKRKTASIVKRDSSAAGTTSSAMMMKVDSAETSVRSQSYESTPVSMDTSPDPPTPIKSPSNSQSQSQPGQQRSVGSLVLLTQKFVDLVKANEGSIDLKAATKILDVQKRRIYDITNVLEGIGLIDKGRHCSLVRWRGGGFNNAKDQENYDLARSRTNHLKMLEDDLDRQLEYAQRNLRYVMQDPSNRSYAYVTRDDLLDIFGDDSVFTIPNYDEEVDIKRNHYELAVSLDNGSAIDIRLVTNQGKSTTNPHDVDGFFDYHRLDTPSPSTSSHSSEDGNAPACAGNVITDEHGYSCNPGMKDEMKLLENELTAKIIFQNYLSGHSLRRFYPDDPNLENPPLLQLNPPQEDFNFALKSDEGICELFDVQCS</INSDQualifier_value> > > </INSDQualifier> > > </INSDFeature_quals> > > </INSDFeature> > > </INSDSeq_feature-table> > > > > <INSDSeq_sequence>AAGAATAGAGGGAGAATGAAAAAAATGACATAAATGGCGGAAAGCAAACCTAGCGCCAACATTCGTATTTTCGTTTAATTTTCGCTCCAAAGTGCAATTAATTCCGGCTTCTTGATCGCTGCATATTGAGTGCAGCCACGCAAAGAGTTACAAGGACAGGAGTATAGTCATCGAGTCGATTGCGGACCATGTACAAGCGCAAAACCGCGAGTATTGTTAAAAGAGACAGCTCCGCAGCGGGCACCACCTCCTCGGCTATGATGATGAAGGTGGATTCGGCTGAGACTTCGGTCCGGTCGCAGAGCTACGAGTCTACACCCGTTAGCATGGACACATCACCGGATCCTCCAACGCCAATCAAGTCTCCGTCGAATTCACAATCGCAATCGCAGCCTGGACAACAGCGCTCCGTGGGCTCACTGGTCCTGCTCACACAGAAGTTTGTGGATCTCGTGAAGGCCAACGAAGGATCCATCGACCTGAAAGCGGCAACCAAAATCTTGGACGTACAGAAGCGCCGAATATACGATATTACCAATGTTTTAGAGGGCATTGGACTAATTGATAAGGGCAGACACTGCTCCCTAGTGCGCTGGCGCGGAGGGGGCTTTAACAATGCCAAGGACCAAGAGAACTACGACCTGGCACGTAGCCGGACTAATCATTTGAAAATGTTGGAGGATGACCTAGACAGGCAACTGGAGTATGCACAGCGCAATCTGCGCTACGTTATGCAGGATCCCTCGAATAGGTCGTATGCATATGTGACACGTGATGATCTGCTGGACATCTTTGGAGATGATTCCGTATTCACAATACCTAATTATGACGAGGAAGTAGATATCAAGCGTAATCATTACGAGCTGGCCGTGTCGCTGGACAATGGCAGCGCAATTGACATTCGCCTGGTGACGAACCAAGGAAAGAGTACTACAAATCCGCACGATGTGGATGGGTTCTTTGACTA! TC! > > ACCGTCTGGACACGCCCTCACCCTCGACGTCGTCGCACTCCAGCGAGGATGGTAACGCTCCAGCATGCGCGGGGAACGTGATCACCGACGAGCACGGTTACTCGTGCAATCCCGGGATGAAAGATGAGATGAAACTTTTGGAGAACGAGCTGACGGCCAAGATAATCTTCCAAAATTATCTGTCCGGTCATTCGCTGCGGCGATTTTATCCCGATGATCCGAATCTAGAAAACCCGCCGCTGCTGCAGCTGAATCCTCCGCAGGAAGACTTCAACTTTGCGTTAAAAAGCGACGAAGGTATTTGCGAGCTGTTTGATGTTCAGTGCTCCTAACTGTGGAAGGGGATGTACACCTTAGGACTATAGCTACACTGCAACTGGCCGCGTGCATTGTGCAAATATTTATGATTAGTACAATTTTGACTTTGGATTTCTCTATATCGTCTAGAAATTTTTAATTAGTGTAATACCTTGTAATTTCGCAAATAACAGCAAAACCAATAAATTCGTAAATGCAAAAAAAAAAAAAAAAAA</INSDSeq_sequence> > > </INSDSeq> > > </INSDSet> > > ================================ > > On 6/6/06, Richard Holland <[EMAIL PROTECTED]> wrote: > >> I can't find any document detailing the differences between INSDseq XML > >> versions 1.3 and 1.4, so I've asked the guys over in the data library > >> section here to see if they have one or can produce one for me. They > >> wrote it so they should know! > >> > >> Once I have this I'll get the INSDseq parser up-to-date. (I could go > >> through the DTDs by hand and work it all out manually, but that would > >> take rather longer than I've got time for at the moment!). > >> > >> It's a bit of a pain trying to keep the parsers up-to-date all the time, > >> especially when people start wanting backwards-compatibility. Does > >> anyone have any bright ideas as to how to manage version changes in file > >> formats? > >> > >> cheers, > >> Richard > >> > >> On Mon, 2006-06-05 at 12:28 -0400, Seth Johnson wrote: > >> > I agree with you on that one. However, the problem might be a little > >> > deeper. Same '?' appear in the INSDseq format bounded by > >> > <INSDReference_reference> tags and cause the following exception. > >> > This tells me that the '?' are actually values that are being > >> > incorrectly parsed. Further examination of the .dtd reveals that > >> > INSDseqFormat.java is tailord towards the INSDSeq v. 1.3 whereas the > >> > files I obtain are in the INSDSeq v. 1.4 (which among other things > >> > contain a new tag <INSDReference_position>). Here're links to both > >> > .dtd's: > >> > > >> > http://www.ebi.ac.uk/embl/Documentation/DTD/INSDSeq_v1.3.dtd.txt > >> > > >> > http://www.ebi.ac.uk/embl/Documentation/DTD/INSDC_V1.4.dtd.txt > >> > > >> > I think it might be worth accommodating changes for the INSDseq > >> > format, not sure how that would affect the '?' in Genbank. > >> > > >> > Seth > >> > > >> > ====================== > >> > 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:348) > >> > Caused by: org.biojava.bio.seq.io.ParseException: > >> > org.biojava.bio.seq.io.ParseException: Bad reference line found: ? > >> > at > >> > org.biojavax.bio.seq.io.INSDseqFormat.readRichSequence(INSDseqFormat.java:250) > >> > at > >> > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109) > >> > ... 1 more > >> > Caused by: org.biojava.bio.seq.io.ParseException: Bad reference line > >> > found: ? > >> > at > >> > org.biojavax.bio.seq.io.INSDseqFormat$INSDseqHandler.endElement(INSDseqFormat.java:901) > >> > at > >> > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:633) > >> > at > >> > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:1241) > >> > at > >> > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(XMLDocumentFragmentScannerImpl.java:1685) > >> > at > >> > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:368) > >> > at > >> > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:834) > >> > at > >> > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:764) > >> > at > >> > com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:148) > >> > at > >> > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1242) > >> > at javax.xml.parsers.SAXParser.parse(SAXParser.java:375) > >> > at org.biojavax.utils.XMLTools.readXMLChunk(XMLTools.java:97) > >> > at > >> > org.biojavax.bio.seq.io.INSDseqFormat.readRichSequence(INSDseqFormat.java:246) > >> > ... 2 more > >> > Java Result: -1 > >> > ====================== > >> > > >> > ~~~~~~~~~~~~~~~~~~~~~~ > >> > <INSDSeq_references> > >> > <INSDReference> > >> > <INSDReference_reference>?</INSDReference_reference> > >> > <INSDReference_position>1..16732</INSDReference_position> > >> > <INSDReference_authors> > >> > <INSDAuthor>Bjornerfeldt,S.</INSDAuthor> > >> > <INSDAuthor>Webster,M.T.</INSDAuthor> > >> > <INSDAuthor>Vila,C.</INSDAuthor> > >> > </INSDReference_authors> > >> > <INSDReference_title>Relaxation of Selective Constraint on Dog > >> > Mitochondrial DNA Following Domestication</INSDReference_title> > >> > <INSDReference_journal>Unpublished</INSDReference_journal> > >> > </INSDReference> > >> > <INSDReference> > >> > <INSDReference_reference>?</INSDReference_reference> > >> > <INSDReference_position>1..16732</INSDReference_position> > >> > <INSDReference_authors> > >> > <INSDAuthor>Bjornerfeldt,S.</INSDAuthor> > >> > <INSDAuthor>Webster,M.T.</INSDAuthor> > >> > <INSDAuthor>Vila,C.</INSDAuthor> > >> > </INSDReference_authors> > >> > <INSDReference_journal>Submitted (06-APR-2006) to the > >> > EMBL/GenBank/DDBJ databases. Evolutionary Biology, Evolutionary > >> > Biology, Norbyvagen 18D, Uppsala 752 36, > >> > Sweden</INSDReference_journal> > >> > </INSDReference> > >> > </INSDSeq_references> > >> > ~~~~~~~~~~~~~~~~~~~~~~ > >> > > >> > On 6/5/06, Richard Holland <[EMAIL PROTECTED]> wrote: > >> > > Hmmm... interesting. I _could_ put in a special case that ignores the > >> > > question marks, but that wouldn't be 'nice' really - this is more of > >> > > a > >> > > problem with the program that is producing the Genbank files than a > >> > > problem with the parser trying to read them. '?' is not a valid tag > >> > > in > >> > > the official Genbank format, and has no meaning attached to it that I > >> > > can work out, so I'm reluctant to make the parser recognise it. > >> > > > >> > > I'd suggest you contact the people who write the software you are > >> > > using > >> > > to produce the Genbank files and ask them if they could stick to the > >> > > rules! > >> > > > >> > > In the meantime you could work around the problem by stripping the > >> > > question marks in some kind of pre-processor before passing it onto > >> > > BioJavaX for parsing. > >> > > > >> > > cheers, > >> > > Richard > >> > > > >> > > On Mon, 2006-06-05 at 11:39 -0400, Seth Johnson wrote: > >> > > > Removing '?' (or several of them in my case) avoids the following > >> > > > 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:348) > >> > > > Caused by: org.biojava.bio.seq.io.ParseException: DQ415957 > >> > > > at > >> > > > org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:245) > >> > > > at > >> > > > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109) > >> > > > ... 1 more > >> > > > Java Result: -1 > >> > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >> > > > I don't know where that previous tokenization problem came from > >> > > > since > >> > > > I can no longer reproduce it. This time it's more or less straight > >> > > > forward. > >> > > > Here's the original file with question marks: > >> > > > ============================ > >> > > > LOCUS DQ415957 1437 bp mRNA linear VRT > >> > > > 01-JUN-2006 > >> > > > DEFINITION Danio rerio capillary morphogenesis protein 2A (cmg2a) > >> > > > mRNA, > >> > > > complete cds. > >> > > > ACCESSION DQ415957 > >> > > > VERSION DQ415957.1 GI:89513612 > >> > > > KEYWORDS . > >> > > > SOURCE Unknown. > >> > > > ORGANISM Unknown. > >> > > > Unclassified. > >> > > > ? > >> > > > ? > >> > > > FEATURES Location/Qualifiers > >> > > > ? > >> > > > gene 1..1437 > >> > > > /gene="cmg2a" > >> > > > CDS 1..1437 > >> > > > /gene="cmg2a" > >> > > > /note="cell surface receptor; similar to > >> > > > anthrax toxin > >> > > > receptor 2 (ANTXR2, ATR2, CMG2)" > >> > > > /codon_start=1 > >> > > > /product="capillary morphogenesis protein 2A" > >> > > > /protein_id="ABD74633.1" > >> > > > /db_xref="GI:89513613" > >> > > > > >> > > > /translation="MTKENLWSVATTATLFFCLCFSSFKAETPSCHGAYDLYFVLDRS > >> > > > > >> > > > GSVSTDWSEIYDFVKNLTERFVSPNLRVSFIVFSSRAEIVLPLTGDRSEINKGLKTLS > >> > > > > >> > > > EVNPAGETYMHEGIKLATEQMKKEPKKSSSIIVALTDGKLETYIHQLTIDEADSARKY > >> > > > > >> > > > GARVYCVGVKDFDEEQLADVADSKEQVFPVKGGFQALKGIVNSILKQSCTEILTVEPS > >> > > > > >> > > > SVCVNQSFDIVLRGNGFAVGRQTEGVICSFIVDGVTYKQKPTKVKIDYILCPAPVLYT > >> > > > > >> > > > VGQQMEVLISLNSGTSYITSAFIITASSCSDGTVVAIVFLVLFLLLALALMWWFWPLC > >> > > > > >> > > > CTVVIKDPPPQRPPPPPPKLEPDPEPKKKWPTVDASYYGGRGAGGIKRMEVRWGEKGS > >> > > > > >> > > > TEEGARLEMAKNAVVSIQEESEEPMVKKPRAPAQTCHQSESKWYTPIRGRLDALWALL > >> > > > RRQYDRVSVMRPTSADKGRCMNFSRTQH" > >> > > > ORIGIN > >> > > > 1 atgacaaagg aaaatctctg gagcgtggca accacggcga ctcttttctt > >> > > > ctgtttatgc > >> > > > 61 ttttcatctt ttaaagcgga aaccccatct tgtcatggtg cctacgacct > >> > > > gtactttgtg > >> > > > 121 ttggaccgat ctggaagtgt ttcgactgac tggagtgaaa tctatgactt > >> > > > tgtcaaaaat > >> > > > 181 cttacagaga gatttgtgag tccaaatctg cgagtgtcct tcattgtttt > >> > > > ttcatcaaga > >> > > > 241 gcagagattg tgttaccgct cactggagac aggtcagaaa ttaataaagg > >> > > > cctgaagacc > >> > > > 301 ttaagtgagg tcaatccagc tggagaaaca tacatgcatg aaggaattaa > >> > > > attggcaact > >> > > > 361 gaacaaatga aaaaagagcc taaaaagtcc tctagtatta ttgtggcctt > >> > > > gactgatgga > >> > > > 421 aagcttgaaa cgtatatcca tcaactcact attgacgagg ctgattcagc > >> > > > aaggaagtat > >> > > > 481 ggggctcgtg tgtactgtgt tggtgtaaaa gactttgatg aagaacagct > >> > > > agccgatgtg > >> > > > 541 gctgattcca aggagcaagt gttcccagtc aaaggaggct ttcaggctct > >> > > > caaaggcatc > >> > > > 601 gttaactcga tcctcaagca atcatgcacc gaaatcctaa cagtggaacc > >> > > > gtccagcgtc > >> > > > 661 tgcgtgaacc agtcctttga cattgttttg agagggaacg ggttcgcagt > >> > > > ggggagacaa > >> > > > 721 acagaaggag tcatctgcag tttcatagtg gatggagtta cttacaaaca > >> > > > aaaaccaacc > >> > > > 781 aaagtgaaga ttgactacat cctatgtcct gctccagtgc tgtatacagt > >> > > > tggacagcaa > >> > > > 841 atggaggttc tgatcagttt gaacagtgga acatcatata tcaccagtgc > >> > > > tttcatcatc > >> > > > 901 actgcctctt catgttcgga cggcacagtg gtggccattg tgttcttggt > >> > > > gctttttctc > >> > > > 961 ctgttggctt tggctctgat gtggtggttc tggcctctat gctgcactgt > >> > > > cgttattaaa > >> > > > 1021 gacccacctc cacaaagacc tcctccacct ccacctaagc tagagccaga > >> > > > cccggaaccc > >> > > > 1081 aagaagaagt ggccaactgt ggatgcatct tactatgggg gaagaggagc > >> > > > tggtggaatc > >> > > > 1141 aaacgcatgg aggtccgttg gggagaaaaa gggtctacag aggaaggtgc > >> > > > aagactagag > >> > > > 1201 atggctaaga atgcagtagt gtcaatacaa gaggaatcag aagaacccat > >> > > > ggtcaaaaag > >> > > > 1261 ccaagagcac ctgcacaaac atgccatcaa tctgaatcca agtggtatac > >> > > > accaatcaga > >> > > > 1321 ggccgtcttg acgcactgtg ggctcttttg cggcggcaat atgaccgagt > >> > > > ttcagttatg > >> > > > 1381 cgaccaactt ctgcagataa gggtcgctgt atgaatttca gtcgcacgca > >> > > > gcattaa > >> > > > // > >> > > > > >> > > > ============================ > >> > > > > >> > > > > >> > > > On 6/5/06, Richard Holland <[EMAIL PROTECTED]> wrote: > >> > > > > Hi again. > >> > > > > > >> > > > > Could you remove the offending question mark from the GenBank > >> > > > > file and > >> > > > > try it again to see if that fixes it? The parser should just > >> > > > > ignore it > >> > > > > but apparently not. The error looks weird to me because the > >> > > > > tokenization > >> > > > > for a DNA GenBank file _does_ contain the letter 't'! Not sure > >> > > > > what's > >> > > > > going on here. > >> > > > ... > >> > > > > > >> > > > > cheers, > >> > > > > Richard > >> > > > > > >> > > > > On Mon, 2006-06-05 at 10:37 -0400, Seth Johnson wrote: > >> > > > > > Hell again Richard, > >> > > > > > > >> > > > > > No sooner I've said about the fix of the last parsing exception > >> > > > > > than > >> > > > > > another one came up with Genbank format: > >> > > > > > -------------------------------------- > >> > > > > > org.biojava.bio.seq.io.ParseException: DQ431065 > >> > > > > > org.biojava.bio.BioException: Could not read sequence > >> > > > > > at > >> > > > > > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112) > >> > > > > > at > >> > > > > > exonhit.parsers.GenBankParser.getGBSequences(GenBankParser.java:151) > >> > > > > > at > >> > > > > > exonhit.parsers.GenBankParser.runGBparser(GenBankParser.java:246) > >> > > > > > at > >> > > > > > exonhit.parsers.GenBankParser.main(GenBankParser.java:326) > >> > > > > > Caused by: org.biojava.bio.seq.io.ParseException: DQ431065 > >> > > > > > at > >> > > > > > org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:245) > >> > > > > > at > >> > > > > > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109) > >> > > > > > ... 3 more > >> > > > > > org.biojava.bio.seq.io.ParseException: > >> > > > > > org.biojava.bio.symbol.IllegalSymbolException: This > >> > > > > > tokenization > >> > > > > > doesn't contain character: 't' > >> > > > > > ---------------------------------------- > >> > > > > > The Genbank file that caused it is as follows: > >> > > > > > ========================================= > >> > > > > > LOCUS DQ431065 425 bp DNA linear > >> > > > > > INV 01-JUN-2006 > >> > > > > > DEFINITION Reticulitermes sp. ALS-2006c 16S ribosomal RNA > >> > > > > > gene, partial > >> > > > > > sequence; mitochondrial. > >> > > > > > ACCESSION DQ431065 > >> > > > > > VERSION DQ431065.1 GI:90102206 > >> > > > > > KEYWORDS . > >> > > > > > SOURCE Vaccinium corymbosum > >> > > > > > ORGANISM Vaccinium corymbosum > >> > > > > > Eukaryota; Viridiplantae; Streptophyta; > >> > > > > > Embryophyta; Tracheophyta; > >> > > > > > Spermatophyta; Magnoliophyta; eudicotyledons; core > >> > > > > > eudicotyledons; > >> > > > > > asterids; Ericales; Ericaceae; Vaccinioideae; > >> > > > > > Vaccinieae; > >> > > > > > Vaccinium. > >> > > > > > ? > >> > > > > > REFERENCE 2 (bases 1 to 425) > >> > > > > > AUTHORS Naik,L.D. and Rowland,L.J. > >> > > > > > TITLE Expressed Sequence Tags of cDNA clones from > >> > > > > > subtracted library of > >> > > > > > Vaccinium corymbosum > >> > > > > > JOURNAL Unpublished (2005) > >> > > > > > FEATURES Location/Qualifiers > >> > > > > > source 1..425 > >> > > > > > /organism="Vaccinium corymbosum" > >> > > > > > /mol_type="genomic DNA" > >> > > > > > /cultivar="Bluecrop" > >> > > > > > /db_xref="taxon:69266" > >> > > > > > /tissue_type="Flower buds" > >> > > > > > /clone_lib="Subtracted cDNA library of > >> > > > > > Vaccinium > >> > > > > > corymbosum" > >> > > > > > /dev_stage="399 hour chill unit exposure" > >> > > > > > /note="Vector: pCR4TOPO; Site_1: Eco R I; > >> > > > > > Site_2: Eco R I" > >> > > > > > rRNA <1..>425 > >> > > > > > /product="16S ribosomal RNA" > >> > > > > > ORIGIN > >> > > > > > 1 cgcctgttta tcaaaaacat cttttcttgt tagtttttga > >> > > > > > agtatggcct gcccgctgac > >> > > > > > 61 tttagtgttg aagggccgcg gtattttgac cgtgcaaagg > >> > > > > > tagcatagtc attagttctt > >> > > > > > 121 taattgtgat ctggtatgaa tggcttgacg aggcatgggc > >> > > > > > tgtcttaatt ttgaattgtt > >> > > > > > 181 tattgaattt ggtctttgag ttaaaattct tagatgtttt > >> > > > > > tatgggacga gaagacccta > >> > > > > > 241 tagagtttaa catttattat ggtccttttc tgtttgtgag > >> > > > > > ggctcactgg gccgtctaat > >> > > > > > 301 atgttttgtt ggggtgatgg gagggaataa tttaacccct > >> > > > > > cctttttatt attatattta > >> > > > > > 361 tttatattta tttgatccat ttattttgat tgtaagatta > >> > > > > > aattacctta gggataacag > >> > > > > > 421 cgtaa > >> > > > > > // > >> > > > > > ================================== > >> > > > > > I think it's the presence of the '?' at the beginning of the > >> > > > > > line?!?! > >> > > > > > I'm not sure wether the information that was supposed to be > >> > > > > > present > >> > > > > > instead of those question marks is absent from the original > >> > > > > > ASN.1 > >> > > > > > batch file or it's a bug in the NCBI ASN2GO software. It looks > >> > > > > > to me > >> > > > > > that the former is the case since the file from NCBI website > >> > > > > > contains > >> > > > > > much more information than the batch file. Just bringing this > >> > > > > > to > >> > > > > > everyone's attention. > >> > > > > > > >> > > > > > > >> > > > > > -- > >> > > > > > Best Regards, > >> > > > > > > >> > > > > > > >> > > > > > Seth Johnson > >> > > > > > Senior Bioinformatics Associate > >> > > > > > > >> > > > > > Ph: (202) 470-0900 > >> > > > > > Fx: (775) 251-0358 > >> > > > > > > >> > > > > > 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. > >> > > > > > ... > >> > > > > > > > >> > > > > > > cheers, > >> > > > > > > Richard > >> > > > > > > > >> > > > > > > > >> > > > > -- > >> > > > > 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 > >> > > > >> > > > >> > > >> > > >> -- > >> Richard Holland (BioMart Team) > >> EMBL-EBI > >> Wellcome Trust Genome Campus > >> Hinxton > >> Cambridge CB10 1SD > >> UNITED KINGDOM > >> Tel: +44-(0)1223-494416 > >> > >> > > > > > > -- > > Best Regards, > > > > > > Seth Johnson > > Senior Bioinformatics Associate > > > > Ph: (202) 470-0900 > > Fx: (775) 251-0358 > > > > _______________________________________________ > > Biojava-l mailing list - [email protected] > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
