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59 lines
1.5 KiB
Perl
59 lines
1.5 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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die "USAGE: $0 CODON_MSA_FILE GUIDANCE_RESIDUE_SCORES_FILE OUT_FILE CUTOFF ALPHABET
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ALPHABET can be either aa or nuc\n" if (@ARGV < 5);
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my ($msaFile,$scoreFile,$outFile,$cutoff,$alphabet) = @ARGV;
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my $missingDataChar;
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if ($alphabet eq "aa") {
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$missingDataChar = "X";
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} elsif ($alphabet eq "nuc") {
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$missingDataChar = "N";
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} else { die "ALPHABET must be either 'aa' or 'nuc'\n" }
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my $in_fasta = Bio::SeqIO->new(-file => $msaFile, '-format' => 'fasta');
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my @seqs;
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my @ids;
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while (my $seqObj = $in_fasta->next_seq()) {
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my @seq_chars = split(//,$seqObj->seq());
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push(@seqs,\@seq_chars);
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push(@ids,$seqObj->id());
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}
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#my $in_fasta = Bio::AlignIO->new(-file => $msaFile , '-format' => 'fasta');
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#my $aln = $in_fasta->next_aln();
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open IN, "<$scoreFile" or die "can't open file $scoreFile";
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#print "cutoff: $cutoff\n";
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while (my $line = <IN>) {#COL_NUMBER #ROW_NUMBER #RES_PAIR_RESIDUE_SCORE
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chomp $line;
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next if ($line =~ m/^#/);
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if ($line =~ m/^\s*(\d+)\s+(\d+)\s+(\S+)$/) {
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if ($3 ne 'nan' and $3 < $cutoff) {
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my $col=$1-1;
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my $row=$2-1;
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$seqs[$row][$col] = $missingDataChar;
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#warn "DEBUG: masking $row,$col\n";
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}
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} else { warn "WARNING: failed to parse line: '$line'\n" }
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}
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close IN;
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open OUT, ">$outFile";
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for (my $i=0; $i<@seqs; ++$i) {
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my $id = $ids[$i];
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my $seqRef=$seqs[$i];
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my @seq_arr = @$seqRef;
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my $seq = join('',@seq_arr);
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print OUT ">$id\n";
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print OUT "$seq\n";
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}
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close OUT;
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