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1 : overbeek 1.1 ########################################################################
2 :    
3 :     use FIG;
4 :     my $fig = new FIG;
5 :     use Sim;
6 :    
7 :     # usage: fast_blastp BlastParms
8 :    
9 :     my $parms = (@ARGV > 0) ? join(" ",@ARGV) : "";
10 :    
11 :     $/ = "\n>";
12 :     while (defined($_ = <STDIN>))
13 :     {
14 :     chomp;
15 :     $/ = "\n";
16 :     if ($_ =~ /^>?(\S+)[^\n]*\n(.*)/s)
17 :     {
18 :     my $id = $1;
19 :     my $seq = $2;
20 :     # print STDERR "processing $id\n";
21 :     $seq =~ s/\s//gs;
22 :     my @sims = $fig->dsims($id,$seq,500,0.1,undef,$parms);
23 :     foreach my $sim (@sims)
24 :     {
25 :     print join("\t",($sim->id1,$sim->id2,$sim->iden,$sim->b1,$sim->e1,$sim->ln1,
26 :     $sim->b2,$sim->e2,$sim->ln2,$sim->psc,$sim->bsc,$sim->nbsc)),"\n";
27 :     }
28 :     }
29 :     $/ = "\n>";
30 :     }

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