[Bioperl-guts-l] [Bug 2172] genbank.pm: parsing of RefSeq NC_004822 crashes

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Jan 1 15:55:23 EST 2007


http://bugzilla.open-bio.org/show_bug.cgi?id=2172





------- Comment #1 from er at xs4all.nl  2007-01-01 15:55 -------
IDACC=NC_004822 perl -Mstrict \
-MLWP::Simple -MIO::String -MBio::SeqIO::genbank \
-e 'print $INC{"Bio/SeqIO/genbank.pm"},"\n\n";' \
-e 'my$val=$ENV{IDACC}; print "getting >$val<\n";' \
-e 'my$url="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$val&cmd=text";'
\
-e 'my$seqio = new Bio::SeqIO(-format=>"genbank",-fh=>
IO::String->new(get($url)));' \
-e 'my$seq = $seqio->next_seq(); ' \
-e 'print $seq->primary_id," / ",$seq->accession_number," 
",$seq->description,"\n\n";'


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