[Biopython-dev] [Bug 2896] New: BLAST XML parser: stripped leading/trailing spaces in Hsp_midline
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Mon Aug 3 16:28:39 UTC 2009
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>
<,Hsp_qseq>XXXXPSPTSLATSHPPLSSMSPYMTI------PQQYLYISKIRSKLSQCALT-RHHH-RELDLRKMV</Hsp_qseq>
<<Hsp_hseq>>EFFEPAITGLYYS-PPLFSVSRLTGLLHLLERPQETLF-TNYRNKIKRLDIPLRHHHIRHLDLEQLV</Hsp_hseq>
<Hsp_midline> P+ T L S PPL S+S + PQ+ L+ + R+K+ + + RHHH R
LDL ++V</Hsp_midline>
</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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