[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JOURNAL Unpublished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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