[Bioperl-guts-l] [Bug 2314] New: Bio:Graphics should handle more gracefully broken GenBank/EMBL formatted files

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Jun 7 17:36:46 EDT 2007


http://bugzilla.open-bio.org/show_bug.cgi?id=2314

           Summary: Bio:Graphics should handle more gracefully broken
                    GenBank/EMBL formatted files
           Product: BioPerl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Unclassified
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: mmokrejs at ribosome.natur.cuni.cz


I use few hours old cvs version ...

$ bp_seqconvert.pl --from genbank --to embl < /mnt/smartmedia/pRL.gb-new4
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
...

But, trying to get a graphics out I get:

$ bp_seqconvert.pl --from genbank --to embl < /mnt/smartmedia/pRL.gb-new4 |
bp_feature_draw.pl
Use of uninitialized value in subtraction (-) at
/usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Panel.pm line 66, <> line 112.
Use of uninitialized value in subtraction (-) at
/usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/FeatureBase.pm line 264, <> line
112.
Use of uninitialized value in subtraction (-) at
/usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/FeatureBase.pm line 264, <> line
112.
�PNG
...


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