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39 lines
1.3 KiB
Perl
39 lines
1.3 KiB
Perl
#!/usr/local/bin/perl -w
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use strict;
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use FileHandle;
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use Bio::SeqIO;
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####################################################################################################################
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# Convert the names in a fasta file to numbers, and creates a code file with the names and the codes (running number)
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###################################################################################################################
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die "Usage: name2codefasta.pl <fastaFile> <codeFile> <outputCodedFile> " if (scalar(@ARGV) < 3);
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my $in_fileName = $ARGV[0];
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my $code_fileName = $ARGV[1];
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my $out_fileName = $ARGV[2];
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my $in_file = Bio::SeqIO->new(-file => $in_fileName , '-format' => 'Fasta');
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my $code_file = new FileHandle(">$code_fileName") or die "Can't write to $code_fileName";
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my $out_file = new FileHandle(">$out_fileName") or die "Can't write to $out_fileName";
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my $counter = 1;
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my $i;
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while ( my $seqObj = $in_file->next_seq() ) {
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my $name = $seqObj->display_id();
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$name.= " ".$seqObj->desc() if ($seqObj->desc());
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print $code_file "$name\t$counter\n";
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my $seq = $seqObj->seq();
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print $out_file ">$counter\n";
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for($i=0;$i<length($seq);$i+=60){
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print $out_file substr($seq,$i,60) . "\n";
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}
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if($i<length($seq)){
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print $out_file substr($seq,$i,length($seq)-$i);
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}
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print $out_file "\n";
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$counter++;
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}
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