[Bioperl-l] Bio::Seq::RichSeq error

Magic Fang fangl at genomics.org.cn
Thu Dec 11 01:59:35 EST 2003


test file:
LOCUS       AY007677                1433 bp    DNA     linear   BCT 29-OCT-2001
DEFINITION  Unknown marine alpha proteobacterium JP66.1 16S ribosomal RNA,
            partial sequence.
ACCESSION   AY007677
VERSION     AY007677.1  GI:12000363
KEYWORDS    .
SOURCE      unknown marine alpha proteobacterium JP66.1
  ORGANISM  unknown marine alpha proteobacterium JP66.1
            Bacteria; Proteobacteria; Alphaproteobacteria.
REFERENCE   1  (bases 1 to 1433)
  AUTHORS   Eilers,H., Pernthaler,J., Peplies,J., Glockner,F.O., Gerdts,G. and
            Amann,R.
  TITLE     Isolation of novel pelagic bacteria from the German bight and their
            seasonal contributions to surface picoplankton
  JOURNAL   Appl. Environ. Microbiol. 67 (11), 5134-5142 (2001)
  MEDLINE   21536174
   PUBMED   11679337
REFERENCE   2  (bases 1 to 1433)
  AUTHORS   Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O., Gerdts,G.,
            Schuett,C. and Amann,R.
  TITLE     Identification and seasonal dominance of culturable marine bacteria
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 1433)
  AUTHORS   Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O., Gerdts,G.,
            Schuett,C. and Amann,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-AUG-2000) Molecular Ecology, Max-Planck-Institute,
            Celsiusstrasse 1, Bremen 28359, Germany
FEATURES             Location/Qualifiers
     source          1..1433
                     /organism="unknown marine alpha proteobacterium JP66.1"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:145652"
     rRNA            <1..>1433
                     /product="16S ribosomal RNA"
ORIGIN
        1 tcatggctca gaacgaacgc tggcggcagg cttaacacat gcaagtcgaa cgatctcttc
       61 ggagatagtg gcagacgggt gagtaacgcg tgggaaccta ccttattcta cggaataaca
      121 gttagaaatg actgctaata ccgtatacgc ccttcggggg aaagatttat cggagtagga
      181 tgggcccgcg ttggattagc tagttggtgg ggtaatggcc taccaaggcg acgatctata
      241 gctggtctga gaggatgatc agccacactg gaactgagac acggtccaga ctcctacggg
      301 aggcagcagt ggggaatatt ggacaatggg cgcaagcctg atccagccat gccgcctgag
      361 tgatgaaggc cttagggttg taaagctctt tcaacggtga agataatgac ggtaaccgta
      421 gaagaagccc cggctaactt cgtgccagca gccgcggtaa tacgaagggg gctagcgttg
      481 ttcggaatta ctgggcgtaa agcgtacgta ggcggattag aaagttaggg gtgaaatccc
      541 agggctcaac cctggaactg cctctaaaac tcctaatctt gagttcgaga gaggtgagtg
      601 gaattccgag tgtagaggtg aaattcgtag atattcggag gaacaccagt ggcgaaggcg
      661 gctcactggc tcgatactga cgctgaggta cgaaagcgtg gggagcaaac aggattagat
      721 accctggtag tccacgccgt aaacgatgaa tgttagccgt cgggcagtat actgttcggt
      781 ggcgcagcta acgcattaaa cattccgcct ggggagtacg gtcgcaagat taaaactcaa
      841 aggaattgac gggggcccgc acaagcggtg gagcatgtgg tttaattcga agcaacgcgc
      901 agaaccttac cagcccttga cataccaatc gcggttagtg gagacacttt ccttcagttc
      961 ggctggattg gatacaggtg ctgcatggct gtcgtcagct cgtgtcgtga gatgttgggt
     1021 taagtcccgc aacgagcgca accctcgcct ttagttgcca gcatttagtt gggcactcta
     1081 gagggactgc cggtgataag ccggaggaag gtggggatga cgtcaagtcc tcatggccct
     1141 tacgggctgg gctacacacg tgctacaatg gtggtgacag tgggcagcga gacggcaacg
     1201 tcgagctaat ctccaaaaac catctcartt cggattgggg tctgcaactc gacccccatg
     1261 aagttggaat cgctagtaat cgcggatcag catgccgcgg tgaatacgtt cccgggcctt
     1321 gtacacaccg cccgtcacac catgggagtt ggtcttaccc gaaggcgatg cgctaaccag
     1381 caatggaggc agtcgaccac ggtagggtca gcgactgggg tgaagtcgta aca
//

test command:
$ perl -e 'use Bio::SeqIO;$in=Bio::SeqIO->new(-file=>"test.gbk", -format=>"genbank");$seq=$in->next_seq;print $seq->dis
play_id, "\t", $seq->species->species, "\n";'

error message:
Can't call method "species" on an undefined value at -e line 1, <GEN0> line 61.

bioperl version 1.3.01



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