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46 lines
1.2 KiB
Perl
46 lines
1.2 KiB
Perl
#!/usr/local/bin/perl
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use Bio::SeqIO;
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use FileHandle;
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use strict;
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###############################################################################################################
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# Takes a fasta MSA file created based on the script names2codeFasta.pl and reverts the codes to the names.
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###############################################################################################################
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die "Usage: $0 <inFile> <codeFile> <outFile> " if (scalar(@ARGV) < 3);
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my ($in_fileName,$code_fileName,$out_fileName) = @ARGV;
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open CODE, "<$code_fileName" or die "Can't open $code_fileName";
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my %codes2names;
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while (my $line=<CODE>){
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$line =~ /(.+)\t(.+)/;
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my $code = $2;
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my $name = $1;
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# print "name: $name \t code: $code \n";
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$codes2names{$code}=$name;
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}
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close CODE;
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open IN, "<$in_fileName" or die "Can't open $in_fileName";
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open OUT, ">$out_fileName" or die "Can't open $out_fileName";
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my %name2seq;
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foreach my $line (<IN>) {
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if ($line =~ m/^>(.*)/) {
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my $code = $1;
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my $new_name = $codes2names{$code};
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# print "$code is replaced with $new_name\n";
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print OUT ">$new_name\n";
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} else {
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print OUT "$line\n";
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}
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}
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close IN;
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close OUT;
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