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

Fabiola Sánchez fsanchez at cifn.unam.mx
Mon Oct 6 14:30:17 EDT 2003


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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