blast_flt

#!/usr/bin/perl
use strict;
use Getopt::Std;
use FindBin;use lib $FindBin::Bin;

my $usage = q{Usage:
 blast_flt [-p minpid] [-l min_qovlen | -q min_qcovs] < blast_tab...
 ..where blast_tab input is expected to have been obtained
 with a blast command with the output format like this:
blastn ... \
 -outfmt '6 qseqid qlen qstart qend sseqid slen sstart send pident bitscore evalue sstrand qcovs salltitles' \
| perl -pe 's/\tminus\t/\t-\t/;s/\tplus\t/\t+\t/' > blast_tab
};
umask 0002;
getopts('p:l:q:o:') || die($usage."\n");
my $outfile=$Getopt::Std::opt_o;
if ($outfile) {
  open(OUTF, '>'.$outfile) || die("Error creating output file $outfile\n");
  select(OUTF);
}
# --
my ($tpid, $talen, $tqcov)=($Getopt::Std::opt_p, $Getopt::Std::opt_l, $Getopt::Std::opt_q);
while (<>) {
 next if m/^#/;
 my $l=$_;
 chomp;
 my ($qid, $qlen, $qstart, $qend, $sid, $slen, $sstart, $send, $pid, $bitscore,
   $evalue, $sstrand, $qcovs, $sdescr) =split(/\t/);
 next if $tpid && $pid<$tpid;
 next if $talen && $qend-$qstart+1<$talen;
 next if $tqcov && $qcovs<$tqcov;
 print $l;
}
# --
if ($outfile) {
 select(STDOUT);
 close(OUTF);
}

#************ Subroutines **************