amit hetawal wrote:
> Hello All,
> I really dont know whats causing this problem. Its like i have the
> input file which looks like:
> And when i see the output there is some difference in the tabs in
> displays. why is that so. Any ideas
>
> sequence : TTCAAGGACTTCTATTCAGAA rev_sequence : TTCTGAATAGAAGTCCTTGAA
> sequence : TCTTGATGAAGAGGAATGGGA rev_sequence : TCCCATTCCTCTTCATCAAGA
> sequence : GCTTGGCAATCTCATGTCAAA rev_sequence : TTTGACATGAGATTGCCAAGC
> sequence : CTAGACCAATGTTTAGTTAGT rev_sequence : ACTAACTAAACATTGGTCTAG
> sequence : TAGTTGTCGTCGTATCTTTGT rev_sequence : ACAAAGATACGACGACAACTA
> sequence : GAGTAAGGCGCTTATCTTCT rev_sequence : AGAAGATAAGCGCCTTACTC
> sequence : TCTGCAACCGGAAAGGGAGC rev_sequence : GCTCCCTTTCCGGTTGCAGA
Looks OK for me:
use strict;
use warnings;
my $filename = $ARGV[0] || 'data/test.dat';
open FILE, "< $filename" or die "Cant open $filename : $!";
while (<FILE>) {
chomp;
next if /^(\s)*$/; # skip blank lines
s/\s+$//g; # remove trailing spaces
my $sequence = $_;
my $compliment = $sequence;
$compliment =~ tr/aAtTcCgGuU/TTAAGGCCTT/;
my $rev_compliment = reverse $compliment;
print "sequence : $sequence\t";
print "rev_sequence : $rev_compliment\n";
}
__END__
sequence : TGCAGAAGAGAGTGAGCAC rev_sequence : GTGCTCACTCTCTTCTGCA
sequence : TGCAGAAGAGAGTGAGCAC rev_sequence : GTGCTCACTCTCTTCTGCA
sequence : TGCAGAAGAGAGTGAGCAC rev_sequence : GTGCTCACTCTCTTCTGCA
sequence : TGCAGAAGAGAGTGAGCAC rev_sequence : GTGCTCACTCTCTTCTGCA
sequence : TGCAGAAGAGAGTGAGCAC rev_sequence : GTGCTCACTCTCTTCTGCA
sequence : TGCAGAAGAGAGTGAGCAC rev_sequence : GTGCTCACTCTCTTCTGCA
sequence : CGCAGAAGAGAGTGAGCACA rev_sequence : TGTGCTCACTCTCTTCTGCG
sequence : TTGCAGAAGAAAGAGAGCAC rev_sequence : GTGCTCTCTTTCTTCTGCAA
sequence : TTGCAGAAGATAGAGAGCAC rev_sequence : GTGCTCTCTATCTTCTGCAA
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