[Bioperl-l] searchIO parse

Thu, 25 Apr 2002 16:02:30 +0800

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As suggested by bioperl1.0,  I am trying to use SearchIO to parse blast =
report.  However, I got the wrong messages as "input file given twice: =
blast and format disagree".   The following is my code:

......=20
my @params=3D('program' =3D> 'blastn', 'database' =3D> $db);
my $factory =3D Bio::Tools::Run::StandAloneBlast->new(@params);
my $input =3D Bio::Seq -> new ('-id' =3D> "test_query", '-seq' =3D> =
$query);
my $blast_report =3D$factory->blastall($input);
my $searchio=3D new Bio::SearchIO('format' =3D> 'blast', '-file' =
=3D>$blast_report);
......

Is there anything wrong?

Thanks!
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Haifeng Liu
Ph.D., Member of Technical Staff

IFL/DS
DSO National Laboratories
20 Science Park Drive
Singapore 118230

Email: lhaifeng@dso.org.sg
Tel: (65) 67728220
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<DIV><FONT face=3DArial size=3D2>As suggested by bioperl1.0,&nbsp; I am =
trying to=20
use SearchIO to parse blast report.&nbsp; However, I got the wrong =
messages as=20
"<STRONG>input file given twice: blast and format=20
disagree</STRONG>".&nbsp;&nbsp; The following is my code:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><STRONG><FONT face=3DArial size=3D2>...... </FONT></STRONG></DIV>
<DIV><STRONG><FONT face=3DArial size=3D2>my @params=3D('program' =3D&gt; =
'blastn',=20
'database' =3D&gt; $db);</FONT></STRONG></DIV>
<DIV><STRONG><FONT face=3DArial size=3D2>my $factory =3D=20
Bio::Tools::Run::StandAloneBlast-&gt;new(@params);</FONT></STRONG></DIV>
<DIV><STRONG><FONT face=3DArial size=3D2>my $input =3D Bio::Seq -&gt; =
new ('-id' =3D&gt;=20
"test_query", '-seq' =3D&gt; $query);</FONT></STRONG></DIV>
<DIV><STRONG><FONT face=3DArial size=3D2>my $blast_report=20
=3D$factory-&gt;blastall($input);</FONT></STRONG></DIV>
<DIV><STRONG><FONT face=3DArial size=3D2>my $searchio=3D new =
Bio::SearchIO('format'=20
=3D&gt; 'blast', '-file' =3D&gt;$blast_report);</FONT></STRONG></DIV>
<DIV><FONT face=3DArial size=3D2><STRONG>......</STRONG></FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Is there anything wrong?</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Thanks!</FONT></DIV>
<DIV><FONT face=3DArial =
size=3D2>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<BR>Haifeng=20
Liu<BR>Ph.D., Member of Technical Staff</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>IFL/DS<BR>DSO National =
Laboratories<BR>20 Science=20
Park Drive<BR>Singapore 118230</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Email: <A=20
href=3D"mailto:lhaifeng@dso.org.sg">lhaifeng@dso.org.sg</A><BR>Tel: (65) =

67728220<BR>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</FONT></DIV></BODY></HTML>

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