[Bio] / FigKernelScripts / fast_blastp.pl Repository:
ViewVC logotype

View of /FigKernelScripts/fast_blastp.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.1 - (download) (as text) (annotate)
Mon Feb 11 16:55:48 2008 UTC (11 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
fast_blastp is a tool to support rapid similarity estimates using FIGfam partitions

########################################################################

use FIG;
my $fig = new FIG;
use Sim;

# usage: fast_blastp BlastParms

my $parms = (@ARGV > 0) ? join(" ",@ARGV) : "";

$/ = "\n>";
while (defined($_ = <STDIN>))
{
    chomp;
    $/ = "\n";
    if ($_ =~ /^>?(\S+)[^\n]*\n(.*)/s)
    {
	my $id = $1;
	my $seq = $2;
#	print STDERR "processing $id\n";
	$seq =~ s/\s//gs;
	my @sims = $fig->dsims($id,$seq,500,0.1,undef,$parms);
	foreach my $sim (@sims)
	{
	    print join("\t",($sim->id1,$sim->id2,$sim->iden,$sim->b1,$sim->e1,$sim->ln1,
			     $sim->b2,$sim->e2,$sim->ln2,$sim->psc,$sim->bsc,$sim->nbsc)),"\n";
	}
    }
    $/ = "\n>";
}

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3