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Re: [Omaha.pm] Issues regarding project objective 1


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@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@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@unmc.edu// <mailto:dbastola@unmc.edu>
//Phone: (402) 559-7720//