[Bioperl-guts-l] [Bug 2305] Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 352, <STDIN> line 4

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Jun 7 10:21:44 EDT 2007


http://bugzilla.open-bio.org/show_bug.cgi?id=2305





------- Comment #6 from mmokrejs at ribosome.natur.cuni.cz  2007-06-07 10:21 EST -------
After the LOCUS line was fixed in current development version of ApE (while
still
DESCRIPTION/ACCESSION/VERSION contain no data == not even the `.') the file can
be parsed by bioperl-live from cvs:

$ bp_seqconvert.pl --from genbank --to embl < /mnt/smartmedia/pRL.gb-new 
ID   unknown; SV 1; linear; unassigned DNA; STD; UNC; 5428 BP.
XX
AC   unknown;
XX
XX
XX
CC   ApEinfo:methylated:1
XX
FH   Key             Location/Qualifiers
FH
FT   misc_feature    589..1449
FT                   /ApEinfo_fwdcolor="#00ff6c"
FT                   /ApEinfo_revcolor="#00ff6c"
FT                   /label=beta-lactamase
FT   misc_feature    2656..3591
FT                   /ApEinfo_fwdcolor="#00ff00"
FT                   /ApEinfo_revcolor="green"
FT                   /label=RLuc
XX
SQ   Sequence 5428 BP; 1534 A; 1174 C; 1312 G; 1408 T; 0 other;
     aaattgtaaa cgtttaatat tttgttaaaa ttcgcgttaa atttttgtta aatcagctca       
60
     ttttttaacc aataggccga aatcggcaaa atcccttata aatcaaaaga atagaccgag      
120
     atagggttga gtgttgttcc agtttggaac aagagtccac tattaaagaa cgtggactcc      
180
     aacgtcaaag ggcgaaaaac cgtctatcag ggcgatggcc cactacgtga accatcaccc      
240
     taatcaagtt ttttggggtc gaggtgccgt aaagcactaa atcggaaccc taaagggatg      
300
     ccccgattta gagcttgacg gggaaagccg gcgaacgtgg cgagaaagga agggaagaaa      
360
     gcgaaaggag cgggcgctag ggcgctggca agtgtagcgg tcacgctgcg cgtaaccacc      
420
     acacccgccg cgcttaatgc gccgctacag ggcgcgtcag gtggcacttt tcggggaaat      
480
     gtgcgcggaa cccctatttg tttatttttc taaatacatt caaatatgta tccgctcatg      
540


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