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>AAGAATAGAGGGAGAATGAAAAAAATGACATAAATGGCGGAAAGCAAACCTAGCGCCAACATTCGTATTTTCGTTTAATTTTCGCTCCAAAGTGCAATTAATTCCGGCTTCTTGATCGCTGCATATTGAGTGCAGCCACGCAAAGAGTTACAAGGACAGGAGTATAGTCATCGAGTCGATTGCGGACCATGTACAAGCGCAAAACCGCGAGTATTGTTAAAAGAGACAGCTCCGCAGCGGGCACCACCTCCTCGGCTATGATGATGAAGGTGGATTCGGCTGAGACTTCGGTCCGGTCGCAGAGCTACGAGTCTACACCCGTTAGCATGGACACATCACCGGATCCTCCAACGCCAATCAAGTCTCCGTCGAATTCACAATCGCAATCGCAGCCTGGACAACAGCGCTCCGTGGGCTCACTGGTCCTGCTCACACAGAAGTTTGTGGATCTCGTGAAGGCCAACGAAGGATCCATCGACCTGAAAGCGGCAACCAAAATCTTGGACGTACAGAAGCGCCGAATATACGATATTACCAATGTTTTAGAGGGCATTGGACTAATTGATAAGGGCAGACACTGCTCCCTAGTGCGCTGGCGCGGAGGGGGCTTTAACAATGCCAAGGACCAAGAGAACTACGACCTGGCACGTAGCCGGACTAATCATTTGAAAATGTTGGAGGATGACCTAGACAGGCAACTGGAGTATGCACAGCGCAATCTGCGCTACGTTATGCAGGATCCCTCGAATAGGTCGTATGCATATGTGACACGTGATGATCTGCTGGACATCTTTGGAGATGATTCCGTATTCACAATACCTAATTATGACGAGGAAGTAGATATCAAGCGTAATCATTACGAGCTGGCCGTGTCGCTGGACAATGGCAGCGCAATTGACATTCGCCTGGTGACGAACCAAGGAAAGAGTACTACAAATCCGCACGATGTGGATGGGTTCTTTGACTATC! > 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 > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
