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Revision 1.1 - (download) (as text) (annotate)
Mon Dec 1 20:46:40 2003 UTC (16 years, 6 months ago) by efrank
Branch: MAIN
CVS Tags: V00-00-01, delong-01, delong-02, V00-00-00

Makefile:
	get it to work with the release tools

All the rest:
	had to rename foo to foo.pl so that makefiles could recognize
	perl source from, say, Makefiles and READMEs

# -*- perl -*-

###########################################
use Carp;
use Data::Dumper;
use FIG_Config;

# -*- perl -*-

# usage: blastp_pseq MinGood [Db] < pseq > table_of_hits

(($cutoff = shift @ARGV) && ($db     = shift @ARGV))
    || die "usage: blastp_pseq MinGood [Db] < pseq > table_of_hits";

$tmp = "$FIG_Config::temp/tmp$$";
open(TMP,">$tmp") || die "could not open $tmp";
while (defined($_ = <STDIN>))
{
    print TMP $_;
}
close(TMP);

$ENV{"BLASTMAT"} = "$FIG_Config::fig/BLASTMAT";
if (! -s "$db.psq")
{
    (system("$FIG_Config::fig/bin/formatdb -i $db -pT") == 0)
	|| die "could not run $FIG_Config::fig/bin/formatdb -i $db";
}

$done = 0;
while (! $done)
{
    if (system("$FIG_Config::fig/bin/blastall -FF -d $db -i $tmp -p blastp > $tmp.out") == 0)
    {
	@tmp = `tail -15 $tmp.out`;
	if ((($tmp[$#tmp] =~ /bits\)\n/s) || (grep(/No hits found/,@tmp) > 0)) && 
	    (system("$FIG_Config::fig/bin/condense_blast $cutoff < $tmp.out > $tmp.out2") == 0) &&
	    open(JOB,"<$tmp.out2"))
	{
	    while (defined($_ = <JOB>))
	    {
		print "blastp,$_";
	    }
	    close(JOB);
	    print "done\n";
	    $done = 1;
	}
    }
}
unlink("$tmp");
unlink("$tmp.out");
unlink("$tmp.out2");

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