[Bioperl-l] Re: [Bioperl-guts-l] How can i get Data from GenBank file

[Jason Stajich]

use Bio::SeqIO;
my $seqio = new Bio::SeqIO(-file => $filename, -format => 'genbank');
my $seq = $seqio->next_seq;
my $species = $seq->species;
see docs on Bio::Species for how to access the fields.
% perldoc Bio::Species

Post these types of questions on bioperl-l in the future please.

-jason

On Wed, 17 Sep 2003, Fabiola [iso-8859-1] Sánchez wrote:

> Hello everybody!
>
> How i can get ORGANISM from genBank file
> and how i can get from FEATURES
> /gene
> /product
> /note
> using Bioperl
> now i using
> use Bio::SeqIO;
>
> Thanks
> Fabi
>
>
> //
> LOCUS       A16STM112               1346 bp    DNA     linear   BCT
> 31-OCT-1996
> DEFINITION  Actinomyces species 16S ribosomal RNA (isolate TM112).
> ACCESSION   X92698
> VERSION     X92698.1  GI:1655518
> KEYWORDS    16S ribosomal RNA; 16S rRNA gene; spacer region.
> SOURCE      Actinomycetales
>   ORGANISM  Actinomycetales
>             Bacteria; Actinobacteria; Actinobacteridae.
> REFERENCE   1
>   AUTHORS   Rheims,H., Sproer,C., Rainey,F.A. and Stackebrandt,E.
>   TITLE     Molecular biological evidence for the occurrence of
> uncultured
>             members of the actinomycete line of descent in different
>             environments and geographical locations
>   JOURNAL   Microbiology (Reading, Engl.) 142 (Pt 10), 2863-2870 (1996)
>   MEDLINE   97039856
>    PUBMED   8885402
> REFERENCE   2  (bases 1 to 1346)
>   AUTHORS   Rheims,H.
>   TITLE     Direct Submission
>   JOURNAL   Submitted (31-OCT-1995) H. Rheims, DSMZ, Deutsche Sammlung
> von
>             Mikroorganismen u. Zellkulturen GmbH, Mascheroder Weg 1b, D-
> 38124
>             Braunschweig, FRG
>   REMARK    Revised by submittor 30-OCT-96
> FEATURES             Location/Qualifiers
>      source          1..1346
>                      /organism="Actinomycetales"
>                      /mol_type="genomic DNA"
>                      /db_xref="taxon:2037"
>                      /clone="TM112"
>      gene            1..1346
>                      /gene="16S rRNA"
>      rRNA            1..1346
>                      /partial
>                      /gene="16S rRNA"
>                      /product="16S ribosomal RNA"
> BASE COUNT      329 a    325 c    422 g    267 t      3 others
> ORIGIN
>         1 cgctggcggc gtgcttaaca catgcaagtc gaacggaatc caaggagctt
> gctccgaaag
>        61 atttagtggc gaacgggtga gtaacacgtg agcaacctgc cccgaagatt
> gggataacac
>       121 cgggaaaccg gtgctaatac cgaataccct caacctgtcg catgacagga
> ggaggaaatg
>       181 tcttatcgct tcgggagggg ctcgcggccc atcagcttgt tggnggggta
> acggcccacc
>       241 aaggcaacga cggatagctg gtctgagagg acgatcagcc acactggaac
> tgagacacgg
>       301 tccagactcc tacgggaggc agcagtgggg aatcttgcgc aatgggcgaa
> agcctgacgc
>       361 agcaacgccg cgtgagggac gaaggctttc tgagttgtaa acctctttcg
> acaggaacga
>       421 ttgtgacggt acctgtagaa gaagcaccgg ccaactatgt gccagcagtc
> gcggtgatac
>       481 atagggtgca agcgttattc ggatttattg ggcgtaaaga gctcgcaggc
> ggntcaacaa
>       541 gtcggntgtt aaacccccag gctcaacctg gggccgccac ctgaaactgt
> tgtgactaga
>       601 gtttggtagg ggatcacgga attcctggtg tagcggtggt atgcgcagat
> atcaggagga
>       661 acaccagtag cgaaggcggt gatctgggcc aatactgacg ctgaggagcg
> aaagcgtggg
>       721 gagcgaacag gattagatac cctggtagtc cacgccgtaa acgttgggca
> ctaggtgtgg
>       781 ggacttttca acggtttcgg tgtcgcaggt aacgcatgaa gtgtcccgcc
> tggggagtac
>       841 ggtcgcaaga ctaaaactca aagaaattga cggtggcccg cacatgcagt
> ggagcatgtg
>       901 gcttatttcg atgcaacgcg aaaaacctta cctagatttg acatgctggg
> aaaagccaca
>       961 gagatgttgt gtccttcggg gcccagcaca ggtggtgcat cgctgtcgtc
> agctcgtgtc
>      1021 gtgagatgtc gcgttaagtc ccgcaacgag cgcaaccctt gttctatgtt
> gccagcacgt
>      1081 aatggcgggg actcgtagaa gactgtcggg gtcaactcgg aggaaggtgg
> ggacgacgtc
>      1141 aagtcatcat gccccttacg tctagggctg cacacatgat acaatgggcg
> gtacagaggg
>      1201 ctgctaaacc gcgaggtgga gccaatccct aaaaccgctc tcagttcaga
> ttgcaggctg
>      1261 caactcgcct gcatgaagtt ggagttgcta gtaatcccgg atcagcattg
> ccggggtgaa
>      1321 tacgttcccg ggccttgtac acaccg
> //
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu