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1 #!/usr/bin/perl
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2 use strict;
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3 use warnings;
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4
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5
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6 my $BLASTResult=$ARGV[0];
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7 my $SEQFile=$ARGV[1];
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8 my $coverage=$ARGV[2];
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9 my $identity=$ARGV[3]*100;#percents
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10 my $score=$ARGV[4];
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11 my %hash;
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12 my @row;
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13 my $line;
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14
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15 #my $coverage=0.5;
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16 #my $identity=50;#percents
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17 #my $score=50;
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18
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19 &ReadSeqLength("$SEQFile",\%hash);
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20
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21 open(F,$BLASTResult);
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22 while ($line=<F>)
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23 {
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24 if ($line!~/\#/)
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25 {
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26 @row=split(/\t/,$line);
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27 if ($row[2]>=$identity and $row[11]>=$score)
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28 {
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29 if ((($row[7]-$row[6]+1)/$hash{$row[0]})>=$coverage)
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30 {
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31 if ((($row[9]-$row[8]+1)/$hash{$row[1]})>=$coverage)
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32 {
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33 print "$row[0]\t$row[1]\t$row[11]";
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34 }
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35 }
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36 }
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37 }
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38 }
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39 close(F);
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40
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41 sub ReadSeqLength()
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42 {
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43 use Bio::SeqIO;
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44 (my $file,my $hash)=@_;
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45 my $seq;
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46 my $in=Bio::SeqIO->new(-file=>"$file",-format=>"fasta");
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47 while ($seq=$in->next_seq())
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48 {
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49 $$hash{$seq->id}=length($seq->seq());
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50 }
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51 } |
