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#!/usr/bin/perl |
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|
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# A script to parse the output of pfam_scan.pl |
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|
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use strict; |
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use File::Basename; |
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|
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# usage |
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unless (@ARGV) |
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{ |
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print "Usage: ./parse_pfam.pl <infile> <outfile>\n"; |
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exit; |
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} |
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|
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my $infile = shift; |
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my $outfile = shift; |
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|
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open (IN, "<$infile") or die "Can't open $infile: $!"; |
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my @lines = <IN>; |
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close IN; |
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|
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open (OUT, ">$outfile") or die "Can't open $outfile: $!"; |
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foreach my $line (@lines) |
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{ |
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# correct place |
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# the start and stop locations are calculated from |
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# the original orf, the locations of which are |
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# in the "trans" file name |
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my @parts = split(/\s+/,$line); |
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my $seq_id = $parts[0]; |
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my $hmm_acc = $parts[3]; |
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my $hmm_start = $parts[4]; |
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my $hmm_end = $parts[5]; |
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my $bit_score = $parts[6]; |
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my $evalue = $parts[7]; |
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my $hmm_name = $parts[8]; |
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my $positions = [split(/\./,$seq_id)]->[-2]; |
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my ($seq_start,$seq_end) = split(/-/,$positions); |
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my $lineout; |
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if ($seq_start < $seq_end) |
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{ |
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$lineout = "$seq_start..$seq_end"; |
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} |
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else |
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{ |
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$lineout = "complement($seq_end..$seq_start)"; |
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} |
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|
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|
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# print to tab file |
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print OUT <<EOF; |
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FT gene $lineout |
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FT /note="PFAM match to $hmm_acc $hmm_start..$hmm_end bit score $bit_score evalue $evalue" |
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FT /label=$seq_id |
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FT /label=$hmm_name |
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FT /score=$bit_score |
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FT /colour=10 155 100 |
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EOF |
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} |
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|
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close OUT; |
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|
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|
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__END__ |
