[Bioperl-l] How can i get lines without tag, next to organism

[Heikki Lehvaslaiho]

Fabiola,

Organism information is put into a Bio::Species object which can be
accessed by $seq->species().

$seq->species->classification() gives you the whole parsed taxomomy
hierarchy from species upwards in an array.

	-Heikki


On Mon, 2003-10-06 at 19:30, Fabiola Sánchez wrote:
> 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.
> 
> 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
> //
> 
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