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Run-blast.pl - Revision history
2024-03-28T09:32:30Z
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Weish: Created page with "This script was used for performing blast search. == Source == <source lang="perl"> #!/usr/bin/perl -w # File: run-blast.pl # Description: # run blast for given query sequence …"
2013-05-05T22:26:58Z
<p>Created page with "This script was used for performing blast search. == Source == <source lang="perl"> #!/usr/bin/perl -w # File: run-blast.pl # Description: # run blast for given query sequence …"</p>
<p><b>New page</b></p><div>This script was used for performing blast search.<br />
<br />
== Source ==<br />
<source lang="perl"><br />
#!/usr/bin/perl -w<br />
# File: run-blast.pl<br />
# Description: <br />
# run blast for given query sequence over big_80 database<br />
# result will be printed out<br />
# Usage:<br />
# run-blast.pl query.fasta [blastp|psiblast] <br />
<br />
use strict;<br />
<br />
use constant DATABASE => '/mnt/project/pracstrucfunc13/data/big/big_80';<br />
<br />
my ($query, $program, $output_type) = ($ARGV[0], undef, undef);<br />
<br />
#parse command line<br />
while ( (my $param = shift @ARGV) ) {<br />
if ($param eq '-p') {<br />
$program = shift @ARGV;<br />
next;<br />
}<br />
<br />
if ($param eq '-m') {<br />
$output_type = shift;<br />
next;<br />
}<br />
}<br />
!$program && ($program = 'blastp');<br />
#TSV output format, without alignment strings<br />
!defined($output_type) && ($output_type = 9);<br />
<br />
#warn "Query:\t$query\n";<br />
#warn "Program:\t$program\n";<br />
#warn "Output:\t$output_type\n";<br />
<br />
#call blastall with given parameters. -b 200000 means maximal number of database<br />
# sequence to be shown<br />
if ($query && -f $query) {<br />
exec "blastall -p $program -d ".DATABASE." -i $query -m $output_type -b 200000";<br />
} else {<br />
#query file is missing, print warning message and show help info<br />
warn "Error: Query file is missing!\n";<br />
warn <br />
"Run blast for given query file against big_80 protein sequence database<br />
Usage: run-blast <query.fasta> -p [blastp|psiblast] -m [0-11]<br />
Parameters:<br />
-p Program to be used for blast (blastp or psiblast)<br />
-m Output format (0 - 11, default is 9). Please consult manual for blastall for details.\n";<br />
exit 1;<br />
}<br />
<br />
__END__<br />
<br />
=head1 run-blast.pl<br />
<br />
Run blast for given query file against big_80 protein sequence database<br />
<br />
=head2 Usage<br />
<br />
run-blast <query.fasta> -p [blastp|psiblast] -m [0-11]<br />
<br />
=head2 Parameters<br />
<br />
=over 4<br />
<br />
=item -p Program to be used for blast (blastp or psiblast)<br />
<br />
=item -m Output format (0 - 11, default is 9). Please consult manual for blastall for details.<br />
<br />
=back<br />
</source></div>
Weish