[Omaha.pm] Issues regarding project objective 1
Jay Hannah
jay at jays.net
Wed Feb 1 19:53:50 PST 2006
Try sending plain text messages to the mailing list. Those HTML emails complete w/ background image will get too big very quickly. -grin-
I'm on a plane right now so I can't look up a specific URL for you, but if you go to
http://search.cpan.org
and search for Bio::Annotation::SimpleValue you should find the documentation for that object. Or, at the command line on your server try
perldoc Bio::Annotation::SimpleValue
or (less likely) the wiki may have something useful
http://bioperl.open-bio.org/wiki/
We've had a death in the family so I'm probably not going to be able to work bioperl this weekend... Hmm, and I don't have access to my schedule right now... I'm probably available next weekend.
Man, the turbulence is baaaaad right now. uck.
j
Dr. Dhundy R. Bastola wrote:
> Hi Jay,
>
> Tried to send this to the list. But sent me back saying it is too big.
> Could we please look into this Bio::Annotation::SipleValue object???
>
> Thanks
>
>
> - Unprocessed:
>
> if there was a word match on the species object. The output is
> messed up for
> the FEATURES? Any suggestion to correct it would be highly appreciated.
>
> Thanks
>
> Kiran
>
> ===============================
> Here is part of my script
> ===============================
> my $outFName= $searchfor.'.gb';
> my $outfile = Bio::SeqIO->new(-file => ">$outFName", -format =>
> 'GenBank');
> foreach (@file_names)
> {
> my $infile = Bio::SeqIO->new(-file => "$_", -format => 'GenBank');
>
> while (my $seq = $infile->next_seq())
> {
> my $species = $seq->species;
> if (grep /$searchfor/i, $species->classification)
> {
> $outfile->write_seq($seq);
> }
> }
> }
> ======================================
>
> - Ignored:
> Here is an example of input file
> =======================================
>
> LOCUS AB005258 332 bp RNA linear VRL
> 22-JUL-1997
> DEFINITION Enterovirus 70 genomic RNA for polyprotein, partial cds.
> ACCESSION AB005258
> VERSION AB005258.1 GI:2274781
> KEYWORDS polyprotein.
> SOURCE Human enterovirus 70
> ORGANISM Human enterovirus 70
> Viruses; ssRNA positive-strand viruses, no DNA stage;
> Picornaviridae; Enterovirus.
> REFERENCE 1 (bases 1 to 332)
> AUTHORS Uchio,E., Yamazaki,K., Aoki,K. and Ohno,S.
> TITLE Detection of enterovirus 70 by polymerase chain reaction in acute
> hemorrhagic conjunctivitis
> JOURNAL Am. J. Ophthalmol. 122 (2), 273-275 (1996)
> PUBMED 8694103
> REFERENCE 2 (bases 1 to 332)
> AUTHORS Yamazaki,K.
> TITLE Direct Submission
> JOURNAL Submitted (26-FEB-1997) Kenji Yamazaki, Osaka Prefectural
> Institute
> of Public Health, Laboratory of Virology; Nakamichi 1-chome
> Higashinari-ku, Osaka, Osaka 537, Japan
> (E-mail:knyamaza at iph.pref.osaka.jp, Tel:06-972-1321(ex.278),
> Fax:06-972-2393)
>
> FEATURES Location/Qualifiers
> source 1..332
> /organism="Human enterovirus 70"
> /mol_type="genomic RNA"
> /isolate="EV70/MNC9/94/Japan"
> /db_xref="taxon:12090"
> /dev_stage="acutely infected"
> CDS <1..>332
> /codon_start=3
> /product="polyprotein"
> /protein_id="BAA21543.1"
> /db_xref="GI:2274782"
> /translation="CMRSFEYKNHSTSTSSIQKNFFIWTLNTRELVQIRRKMELFTYL
> RFDTEITIVPTLRLFSSSNVSFSGLPNLTLQAMYVPVGAPKPSSQDSFEWQSACNPSV
> FFKINDPP"
> ==================================
> Here is an example of output file
> ==================================
> LOCUS AB005258 332 bp RNA linear VRL
> 22-JUL-1997
> DEFINITION Enterovirus 70 genomic RNA for polyprotein, partial cds.
> ACCESSION AB005258
> VERSION AB005258.1 GI:2274781
> KEYWORDS polyprotein.
> SOURCE Human enterovirus 70
> ORGANISM Enterovirus Human enterovirus 70
> Viruses; ssRNA positive-strand viruses, no DNA stage;
> Picornaviridae; Enterovirus.
> REFERENCE 1 (bases 1 to 332)
> AUTHORS Uchio,E., Yamazaki,K., Aoki,K. and Ohno,S.
> TITLE Detection of enterovirus 70 by polymerase chain reaction in
> acute
> hemorrhagic conjunctivitis
> JOURNAL Am. J. Ophthalmol. 122 (2), 273-275 (1996)
> PUBMED 8694103
> REFERENCE 2 (bases 1 to 332)
> AUTHORS Yamazaki,K.
> TITLE Direct Submission
> JOURNAL Submitted (26-FEB-1997) Kenji Yamazaki, Osaka Prefectural
> Institute of Public Health, Laboratory of Virology;
> Nakamichi
> 1-chome Higashinari-ku, Osaka, Osaka 537, Japan
> (E-mail:knyamaza at iph.pref.osaka.jp, Tel:06-972-1321(ex.278),
> Fax:06-972-2393)
> FEATURES Location/Qualifiers
> source 1..332
> /db_xref="Bio::Annotation::SimpleValue=HASH(0x8707e84)"
> /mol_type="Bio::Annotation::SimpleValue=HASH(0x8702c0c)"
> /isolate="Bio::Annotation::SimpleValue=HASH(0x870b05c)"
> /dev_stage="Bio::Annotation::SimpleValue=HASH(0x86f9a84)"
> /organism="Bio::Annotation::SimpleValue=HASH(0x877ce5c)"
> CDS <1..>332
> /db_xref="Bio::Annotation::SimpleValue=HASH(0x86f5fec)"
> /codon_start=Bio::Annotation::SimpleValue=HASH(0x8702c48)
> /protein_id="Bio::Annotation::SimpleValue=HASH(0x8705ea8)"
> /translation="Bio::Annotation::SimpleValue=HASH(0x870de5c)
> /product="Bio::Annotation::SimpleValue=HASH(0x87080dc)"
> BASE COUNT 100 a 74 c 60 g 98 t
>
>
> //Dr. Dhundy R. Bastola//
> //Assistant Professor//
> //Department of Pediatrics//
> //University of Nebraska Medical Center//
> //Omaha//// NE 68198//
> //E-mail: ////dbastola at unmc.edu// <mailto:dbastola at unmc.edu>
> //Phone: (402) 559-7720//
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