[Omaha.pm] Issues regarding project objective 1

[Jay Hannah]

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//