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executable file 80 lines (65 sloc) 2.294 kB
#!/usr/bin/perl
#
################################################################################
#11-17-2001
#Jianwen Fang (jwfang1999@yahoo.com)
#
#THis program returns reverse complement sequences of all sequences in the current directory
#and save them in the same directory, using the same name with extension ".rev"
###############################################################################
use strict;
use Bio::Seq;
use Bio::SeqIO;
my @files = ();
my $folder = '.';
my $inputFormat;
my $outputFormat;
my $numSeq;
#Fasta FASTA format
#EMBL EMBL format
#GenBank GenBank format
#GCG GCG format
#raw Raw format (one sequence per line, no ID)
my @format = ('Fasta', 'EMBL', 'GenBank', 'GCG', 'Raw');
print("\nWhat is the format of the original sequence files?\n");
print("type 0 for Fasta; 1 for EMBL; 2 for GenBank; 3 for GCG; 4 for Raw\n");
$inputFormat = <STDIN>;
chomp ($inputFormat);
print("\nWhat is the format of the reverse complement sequence files you want?\n");
print("type 0 for Fasta; 1 for EMBL; 2 for GenBank; 3 for GCG; 4 for Raw\n");
$outputFormat = <STDIN>;
chomp ($outputFormat);
unless(opendir(FOLDER, $folder))
{
print "cannot open folder $folder!\n";
exit;
}
@files = grep(!/^\.\.?$/, readdir(FOLDER));
foreach my $file (@files)
{
if($file =~ /seq/i)
{
getRevcom($file);
$numSeq++;
}
}
print "$numSeq reverse complement sequences have been saved in current directory\n";
exit;
############################################################################
#subroutine getRevcom take an backward sequence file name(should with .seq extension) as parameter
#return its revcom sequence using the same name with the extension replaced with rev
############################################################################
sub getRevcom
{
my $seqFile = $_[0];
my $in = Bio::SeqIO->new('-file'=>$seqFile, '-format'=>$format[$inputFormat]);
my $seq = $in->next_seq();
my $revcomSeq = $seq->revcom();
my @outSeqFile = split (/\./, $seqFile);
pop @outSeqFile;
push(@outSeqFile, 'rev');
my $outSeqFile = join('.', @outSeqFile);
print "$outSeqFile\n";
my $out = Bio::SeqIO->new('-file'=>">$outSeqFile", '-format'=>$format[$outputFormat]);
$out->write_seq($revcomSeq);
}
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