[Biojava-l] Parsing INSDseq Sequences (1.3 & 1.4)
Seth Johnson
johnson.biotech at gmail.com
Tue Jun 13 16:28:24 UTC 2006
Works like a charm now!!! :) I figured it was a typo somewhere on Friday,
but couldn't find the source. I didn't think tag info was case sensitive.
On 6/12/06, Richard Holland <richard.holland at ebi.ac.uk> wrote:
>
> Typo in code. my fault. Try again!
>
>
>
> On Thu, 2006-06-08 at 10:23 -0400, Seth Johnson wrote:
> > I'm still getting an empty array back from this:
> >
> > Note [] myAccs = ((RichAnnotation)rs.getAnnotation()).getProperties
> > (INSDseqFormat.Terms.getOtherSeqIdTerm());
> >
> > Here's the file that I'm parsing:
> > ~~~~~~~~~~~~~~~~~~~~~~
> > <?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
> > cdna at fruitfly.berkeley.edu.</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>AAGAATAGAGGGAGAATGAAAAAAATGACATAAATGGCGGAAAGCAAACCTAGCGCCAACATTCGTATTTTCGTTTAATTTTCGCTCCAAAGTGCAATTAATTCCGGCTTCTTGATCGCTGCATATTGAGTGCAGCCACGCAAAGAGTTACAAGGACAGGAGTATAGTCATCGAGTCGATTGCGGACCATGTACAAGCGCAAAACCGCGAGTATTGTTAAAAGAGACAGCTCCGCAGCGGGCACCACCTCCTCGGCTATGATGATGAAGGTGGATTCGGCTGAGACTTCGGTCCGGTCGCAGAGCTACGAGTCTACACCCGTTAGCATGGACACATCACCGGATCCTCCAACGCCAATCAAGTCTCCGTCGAATTCACAATCGCAATCGCAGCCTGGACAACAGCGCTCCGTGGGCTCACTGGTCCTGCTCACACAGAAGTTTGTGGATCTCGTGAAGGCCAACGAAGGATCCATCGACCTGAAAGCGGCAACCAAAATCTTGGACGTACAGAAGCGCCGAATATACGATATTACCAATGTTTTAGAGGGCATTGGACTAATTGATAAGGGCAGACACTGCTCCCTAGTGCGCTGGCGCGGAGGGGGCTTTAACAATGCCAAGGACCAAGAGAACTACGACCTGGCACGTAGCCGGACTAATCATTTGAAAATGTTGGAGGATGACCTAGACAGGCAACTGGAGTATGCACAGCGCAATCTGCGCTACGTTATGCAGGATCCCTCGAATAGGTCGTATGCATATGTGACACGTGATGATCTGCTGGACATCTTTGGAGATGATTCCGTATTCACAATACCTAATTATGACGAGGAAGTAGATATCAAGCGTAATCATTACGAGCTGGCCGTGTCGCTGGACAATGGCAGCGCAATTGACATTCGCCTGGTGACGAACCAAGGAAAGAGTACTACAAATCCGCACGATGTGGATGGGTTCTTTGACTATCACCGTCTGGACACGCCCTCACCCTCGACGTCGTCGCACTCCAGCGAGGATGGTAACGCTCCAGCATGCGCGGGGAACGTGATCACCGACGAGCACGGTTACTCGTGCAATCCCGGGATGAAAGATGAGATGAAACTTTTGGAGAACGAGCTGACGGCCAAGATAATCTTCCAAAATTATCTGTCCGGTCATTCGCTGCGGCGATTTTATCCCGATGATCCGAATCTAGAAAACCCGCCGCTGCTGCAGCTGAATCCTCCGCAGGAAGACTTCAACTTTGCGTTAAAAAGCGACGAAGGTATTTGCGAGCTGTTTGATGTTCAGTGCTCCTAACTGTGGAAGGGGATGTACACCTTAGGACTATAGCTACACTGCAACTGGCCGCGTGCATTGTGCAAATATTTATGATTAGTACAATTTTGACTTTGGATTTCTCTATATCGTCTAGAAATTTTTAATTAGTGTAATACCTTGTAATTTCGCAAATAACAGCAAAACCAATAAATTCGTAAATGCAAAAAAAAAAAAAAAAAA</INSDSeq_sequence>
>
> > </INSDSeq>
> > </INSDSet>
> > ~~~~~~~~~~~~~~~~~~~~~~
> >
> > On 6/8/06, Richard Holland <richard.holland at ebi.ac.uk> wrote:
> > Yesterday I think I said I was going to add other-seqids but I
> > forgot to
> > do it, so I did it just now. Try it and see. Use the new
> > INSDseqFormat.Terms.getOtherSeqIdTerm() term to find them.
> >
> > cheers,
> > Richard
> >
> > On Wed, 2006-06-07 at 19:48 -0400, Seth Johnson wrote:
> > > Hi Richard,
> > >
> > > I still cannot locate the GI number for the main
> > sequence. After I
> > > parse it with readINSDseqDNA, I then use:
> > >
> > > Note [] myAccs =
> > ((RichAnnotation)rs.getAnnotation
> > > ()).getProperties( Terms.getAdditionalAccessionTerm ());
> > >
> > > However, the 'myAccs' appears to be empty. Am I on the
> > wrong track to
> > > get to other-seqids???
> > >
> > > On 6/6/06, Richard Holland < richard.holland at ebi.ac.uk>
> > wrote:
> > > GenBank has a separate line for GI number, so it can
> > be parsed
> > > out
> > > nicely. INSDseq does not, so you have to rely on the
> > other-
> > > seqids tag
> > > and hope that one of them is the GI number. However
> > it seems I
> > > have not
> > > included that tag in the parser, so I will include
> > it. This
> > > will make
> > > the other-seqids values available through the notes
> > with the
> > > term
> > > Terms.getAdditionalAccessionTerm(), but
> > getIdentifier() will
> > > remain
> > > null.
> > >
> > > For your second question, the tutorial makes the
> > mistake in
> > > several
> > > places of saying getNoteSet( Terms.blahblah()). This
> > was
> > > shorthand for:
> > >
> > > rs.getAnnotation().getProperty(Terms.blahblah())
> > > (for single values)
> > >
> > > or
> > >
> > > ((RichAnnotation)rs.getAnnotation()).getProperties
> > > ( Terms.blahblah ())
> > > (for multiple values)
> > >
> > > but never got expanded. Maybe someone can fix that
> > one
> > > day... :)ded...
> > >
> > > I'm just updating INSDseq to 1.4 now. The guys next
> > door gave
> > > me the
> > > details of the changes, and told me that 1.3 is
> > actually no
> > > longer
> > > supported by them after Friday this week! So I'll
> > make it 1.4
> > > only.
> > >
> > > cheers,
> > > Richard
> > >
> > --
> > 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
> --
> 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
--
Best Regards,
Seth Johnson
Senior Bioinformatics Associate
Ph: (202) 470-0900
Fx: (775) 251-0358
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