[Bioperl-l] How can i get ...

[Marc Logghe]

Hi,
it is like Heikki already mentioned, you need the classification() method of Bio::Species.
You get the output 
"Bacteria; Proteobacteria; Gammaproteobacteria; Oceanospirillales; Pseudospirillum"
when you run the code:
my $species = $seq->species;
my @classification = reverse $species->classification;
pop @classification;
print join( '; ', @classification), "\n";

ML
> -----Original Message-----
> From: Fabiola Sánchez [mailto:fsanchez at cifn.unam.mx]
> Sent: Monday, October 06, 2003 8:25 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] How can i get ...
> 
> 
> Hello!
> I'm reading  files in genbank format
> i want to parser the lines below  or next to organism, but 
> these don't 
> have tag
> how can i get this
> i can get organism but  i can't get the lines next to organism
> for example:
> 
> ORGANISM  Pseudospirillum japonicum
>             Bacteria; Proteobacteria; Gammaproteobacteria; 
> Oceanospirillales;
>             Pseudospirillum.
> I need to get: 
>             Bacteria; Proteobacteria; Gammaproteobacteria; 
> Oceanospirillales;
>             Pseudospirillum.
> but i can't
> 
> Thank you.
> 
> Fabi
> 
> 
> 
> LOCUS       AB006766                1459 bp    DNA     linear   BCT 
> 13-FEB-1999
> DEFINITION  Oceanospirillum japonicum gene for 16S rRNA, 
> partial sequence,
>             strain:IFO19191.
> ACCESSION   AB006766
> VERSION     AB006766.1  GI:4049363
> KEYWORDS    16S ribosomal RNA.
> SOURCE      Pseudospirillum japonicum
>   ORGANISM  Pseudospirillum japonicum
>             Bacteria; Proteobacteria; Gammaproteobacteria; 
> Oceanospirillales;
>             Pseudospirillum.
> REFERENCE   1  (sites)
>   AUTHORS   Satomi,M., Kimura,B., Hayashi,M., Shouzen,Y., 
> Okuzumi,M. and
>             Fujii,T.
>   TITLE     Marinospirillum gen. nov., with descriptions of 
> Marinospirillum
>             megaterium sp. nov., isolated from kusaya gravy, 
> and transfer of
>             Oceanospirillum minutulum to Marinospirillum 
> minutulum comb. nov
>   JOURNAL   Int. J. Syst. Bacteriol. 48 Pt 4, 1341-1348 (1998)
>   MEDLINE   99045875
>    PUBMED   9828435
> REFERENCE   2  (bases 1 to 1459)
>   AUTHORS   Satomi,M.
>   TITLE     Direct Submission
>   JOURNAL   Submitted (20-AUG-1997) Masataka Satomi, National Reserch 
> Institute
>             of Fisheries Science, Food Processing and 
> Preservation Division;
>             Fukuura 2-12-4, Kanazawa-ku,, Yokohama, Kanagawa 
> 236, Japan
>             (E-mail:msatomi at nrifs.affrc.go.jp, Tel:81-45-788-7670,
>             Fax:81-45-788-7670)
> FEATURES             Location/Qualifiers
>      source          1..1459
>                      /organism="Pseudospirillum japonicum"
>                      /mol_type="genomic DNA"
>                      /strain="ATCC19191"
>                      /db_xref="taxon:64971"
>      rRNA            <1..>1459
>                      /product="16S ribosomal RNA"
> BASE COUNT      368 a    326 c    462 g    302 t      1 others
> ORIGIN     
>         1 attgaacgct ggcggcaggc ctaacacatg caagtcgagc 
> ggcagcgggg agtagcttgc
>        61 tactttgccg gcgagcggcg gacgggtgag taacgcatag 
> gaatctgccc agtagagggg
>       121 gatagccagg ggaaactctg attaataccg catacgccct 
> acgggggaaa aggggctttt
>       181 agctcctgct attggatgag cctatgtcgg attagctagt 
> tggtagggta aaggcctacc
>       241 aaggcgacga tccgtagctg ttctgagagg atgatcagcc 
> acactgggac tgagacacgg
>       301 cccagactcc tacgggaggc agcagtgggg aatattgcac 
> aatgggggga accctgatgc
>       361 acccatcccg cgtgtgtgaa gaaggccttc gggttgtaaa 
> gcactttcag caaggaggaa
>       421 ggccgtatgc ttaataggca tgcggattga cgttacttgc 
> agaagaagca ccggctaact
>       481 ccgtgccagc agccgcggta atacggaggg tgcgagcgtt 
> aatcggaatt actgggcgta
>       541 aagcgcgcgt aggcggatag gtcagtcaga tgtgaaagcc 
> ctgggctcaa cctaggacgt
>       601 gcacctgata ctgcttatct agagtaaggt agagggtagt 
> agaatttcct gtgtagcggt
>       661 gaaatgcgta gatataggaa ggaataccgg tggcgaaggc 
> ggctacctgg actattactg
>       721 acgctgaggt gcgaaagcgt ggggatcaaa caggattaga 
> taccctggta gtccacgctg
>       781 taaacgatgt cgactagccg ttgccgacct tgagttggga 
> gtggcgcagc taacgcgata
>       841 agtcgaccgc ctggggagta cggccgcaag gttaaaactc 
> aaatgaattg acgggggccc
>       901 gcacaagcgg tggagcatgt ggtttaattc gatgcaacgc 
> gaagaacctt acctactctt
>       961 gacatccaga gaactttcca gagatggata ggtgccttcg 
> ggaactctga gacaggtgct
>      1021 gcatggctgt cgtcagctcg tgttgtgaaa tgttgggtta 
> agtcccgtaa cgagcgcaac
>      1081 ccttatcctt atttgccagc gggttatgcc gggaacttta 
> aggaaactgc cggtgacaaa
>      1141 ccggaggaag gtggggacga cgtcaagtca tcatggccct 
> tacgagtagg gctacacacg
>      1201 tgctacaatg gtaagtacag agggttgcaa gaccgcgagg 
> tggagctaat ctcagaaaac
>      1261 ttatcgtagt ccggattgga gtctgcaact cgactccatg 
> aagtcggaat cgctagtaat
>      1321 cgcgaatcag aatgtcgcgg tgaatacgtt cccgggcctt 
> gtacacaccg cccgtcacac
>      1381 catgggagtg gacttcacca gaagtagtta gtctaaccgn 
> aagggggacg attaccacgg
>      1441 tggggttcat gactggggt
> //
>