[Biopython-dev] [Bug 2896] New: BLAST XML parser: stripped leading/trailing spaces in Hsp_midline

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2896

           Summary: BLAST XML parser: stripped leading/trailing spaces in
                    Hsp_midline
           Product: Biopython
           Version: 1.50
          Platform: All
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: volkmer at mpi-cbg.de


Parsing a XML output file from NCBI BLAST using blastp & complexity filters on
omits leading/trailing spaces in the hsp match line: 

hsp.query
u'XXXXPSPTSLATSHPPLSSMSPYMTI------PQQYLYISKIRSKLSQCALT-RHHH-RELDLRKMV'
hsp.match
u'P+ T L  S PPL S+S    +      PQ+ L+ +  R+K+ +  +  RHHH R LDL ++V'

This makes it more awkward to evaluate the alignment. It would be the best when
query, subject and alignment always have the same length. The BLAST XML output
file at least has the correct Hsp_midline:

<pre>
&lt,Hsp_qseq&gt;XXXXPSPTSLATSHPPLSSMSPYMTI------PQQYLYISKIRSKLSQCALT-RHHH-RELDLRKMV&lt;/Hsp_qseq&gt;
<&lt;Hsp_hseq>&gt;EFFEPAITGLYYS-PPLFSVSRLTGLLHLLERPQETLF-TNYRNKIKRLDIPLRHHHIRHLDLEQLV&lt;/Hsp_hseq&gt;
&lt;Hsp_midline&gt;    P+ T L  S PPL S+S    +      PQ+ L+ +  R+K+ +  +  RHHH R
LDL ++V&lt;/Hsp_midline&gt;
</pre>

And as the plaintext parser gives the complete alignment line it would be nice
to get the same behaviour.

Thanks,
Michael


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