[Biojava-l] Parsing INSDseq Sequences (1.3 & 1.4)
Seth Johnson
johnson.biotech at gmail.com
Thu Jun 8 14:23:17 UTC 2006
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
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