[Bioperl-guts-l] [Bug 3058] New: Bio::SearchIO is unable to parse fasta35 output

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Apr 14 09:55:57 EDT 2010


http://bugzilla.open-bio.org/show_bug.cgi?id=3058

           Summary: Bio::SearchIO is unable to parse fasta35 output
           Product: BioPerl
           Version: 1.6 branch
          Platform: Other
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P1
         Component: Bio::Search/Bio::SearchIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: michael.watson at bbsrc.ac.uk


I have two versions of Bioperl, 1.6.0 and 1.6.1

I have a very large fasta35 output file (10,000s of searches).

When I try a simple parsing of this file using Bio::SearchIO, I get the
following:

1.6.0
-------
Multiple warning messages of the kind:
--------------------- WARNING ---------------------
MSG: Unrecognized alignment line (1) ' /usr/local/fasta3/bin/fasta35 -n -U -Q
-H -A -E 2.0 -C 19 -m 0 -m 9i test.fa ../other_mirs.fa -O test.fasta35'
---------------------------------------------------

1.6.1
-------
A single stack trace:
------------- EXCEPTION -------------
MSG: Unrecognized alignment line (1) ' /usr/local/fasta3/bin/fasta35 -n -U -Q
-H -A -E 2.0 -C 19 -m 0 -m 9i test.fa ../other_mirs.fa -O test.fasta35'
STACK Bio::SearchIO::fasta::next_result
/usr/local/BioPerl-1.6.1/Bio/SearchIO/fasta.pm:1333
STACK toplevel test_6.1.pl:9
-------------------------------------

Further analysis seems to suggest that whenever the warning message is flashed
up, that particular SearchIO object is not created.


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