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<DIV><FONT face=Arial size=2>Hello.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I'm trying to parse the results of a blast query,
using BPLite. The problem is: I can't access the evalue of a HSP. For
accessing the score, there are no problems: I only have to access the HSP's
field "score. But... what with evalue? If I do the same using "evalue", there's
an error: it can't find that field on the HSP.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Here you can see the main part of the
code:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>$factory =
Bio::Tools::Run::StandAloneBlast->new(@pars); <BR>my $blst_rprt =
$factory->blastall($seq);<BR>my $exists_results =
parse_blast($blst_rprt);</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>And the function parse_blast is
this:</FONT></DIV><FONT face=Arial size=2>
<DIV><BR>sub parse_blast {<BR>my $blast_report = shift;</DIV>
<DIV> </DIV>
<DIV> while (my $result = $blast_report->nextSbjct) {</DIV>
<DIV> while ( my $hsp = $result->nextHSP ) </DIV>
<DIV> {</DIV>
<DIV> my $score = $hsp->score;</DIV>
<DIV> my $evalue = $hsp->evalue;</DIV>
<DIV> }</DIV>
<DIV> }</DIV>
<DIV> </DIV>
<DIV>}</DIV>
<DIV> </DIV>
<DIV>A different problem (although closely related with the one above) i'd like
to ask is this:</DIV>
<DIV>I thought that maybe it'd be better to use SearchIO for the
parsing, but then the problem is that when creating a SearchIO variable, you
have to pass the name of the file where the blast result to parse is. But as you
can see in the code, my blast result is in the variable $blst_rprt (or
$blast_report), not in a file. So should I write the content of the
$blast_report variable into a file, and pass this file to SearchIO? I don't like
this solution; i would be grateful if you could give me an alternative
one.</DIV>
<DIV> </DIV>
<DIV>Thank you in advance.</DIV>
<DIV> </DIV></FONT>
<DIV><FONT face=Arial size=2>--<BR>David García Cortés<BR>Instituto Nacional de
Bioinformática (INB)<BR>Nodo Computacional GNHC-2 UPC-CIRI<BR>c/. Jordi Girona
1-3
<BR>Modul
C6-E201
Tel. : 934 011 650<BR>E-08034
Barcelona
Fax : 934 017 014<BR>Catalunya
(Spain)
e-mail: <A
href="mailto:davidg@lsi.upc.edu">davidg@lsi.upc.edu</A><BR></FONT></DIV></BODY></HTML>