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52 lines
1.2 KiB
Perl
52 lines
1.2 KiB
Perl
#!/usr/bin/perl -w
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use strict;
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use Bio::SeqIO;
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use Bio::Align::AlignI;
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use Bio::AlignIO;
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use warnings;
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# no checks of the input files are done.
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die "USAGE: $0 MSA_FILE SP_FILE OUT_FILE CUTOFF" if (@ARGV < 4);
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my ($msaFile,$spFile,$outFile,$cutoff) = @ARGV;
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my $in_fasta = Bio::SeqIO->new(-file => $msaFile, '-format' => 'fasta');
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my @seqs;
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# read the file into an array
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while (my $seqObj = $in_fasta->next_seq()) {
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push(@seqs,$seqObj);
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}
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open IN, "<$spFile" or die "can't open file $spFile";
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open OUT, ">$outFile";
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my $numRemovedPos = 0;
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foreach my $line(<IN>) {
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if ($line =~ m/^\s*(\d+)\s+(\d+(\.\d+)?)/) {
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if ($2 < $cutoff) {
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removePos($1);
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}
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}
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}
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foreach my $seqObj (@seqs) {
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my $id = $seqObj->id();
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my $seq = $seqObj->seq();
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print OUT ">$id\n$seq\n";
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}
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sub removePos {
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print "removed pos $_[0]\n";
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my $pos2remove = $_[0] - $numRemovedPos;
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foreach my $seqObj (@seqs) {
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my $new_seq = "";
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if ($pos2remove>1) {
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$new_seq = $seqObj->subseq(1,$pos2remove-1);
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}
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if ($pos2remove< $seqObj->length()) {
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$new_seq .= $seqObj->subseq($pos2remove+1,$seqObj->length());
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}
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$seqObj->seq($new_seq);
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}
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$numRemovedPos++;
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}
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