[Bioperl-guts-l] [Bug 2888] New: When reading blast results: spaces at end of line in multi-line query description are lost

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue Jul 28 11:00:15 EDT 2009


http://bugzilla.open-bio.org/show_bug.cgi?id=2888

           Summary: When reading blast results:  spaces at end of line in
                    multi-line query description are lost
           Product: BioPerl
           Version: 1.6 branch
          Platform: Other
        OS/Version: Linux
            Status: NEW
          Severity: minor
          Priority: P2
         Component: Bio::Search/Bio::SearchIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: eyal.privman at gmail.com


I use Bio::SearchIO from BioPerl version 1.6 to read results of NCBI BLAST
version 2.2.16, where the description of the query sequence (that was
originally the fasta header line) was broken to several lines.  See example
below.  When I use:
$result = $blastIO->next_result
$result->query_description
I get the description as one string, but no space is separation the last word
on the line from the first word on the next line.  (In the example below "gene"
and "for" will be "genefor")

This doesn't happen with bioperl 1.5.2 - I get the description with a space
between the two words.

Example blast input:

TBLASTX 2.2.16 [Mar-25-2007]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= dbj|AB027451.1|_TRUNC_466_3843 Saccharomyces bayanus HO gene
for endonuclease for mating-type conversion, complete cds
         (3378 letters)
...
...
...


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