Just wondering why not use BioPerl (www.bioperl.org)?
Nath
amit hetawal wrote:
> Hello All,
> I really dont know whats causing this problem. Its like i have the
> input file which looks like:
>
> :set list on in vi
>
> TGCAGAAGAGAGTGAGCAC$
> TGCAGAAGAGAGTGAGCAC $
> TGCAGAAGAGAGTGAGCAC $
> TGCAGAAGAGAGTGAGCAC $
> TGCAGAAGAGAGTGAGCAC $
> TGCAGAAGAGAGTGAGCAC $
> CGCAGAAGAGAGTGAGCACA$
> TTGCAGAAGAAAGAGAGCAC$
> TTGCAGAAGATAGAGAGCAC$
>
> (there are some trailing spaces in above sequences.)
>
> And when i use the below script:
>
> $filename = $ARGV[0];
> open (FILE, "< $filename") or die "Cant open $filename : $!";
>
> $sequence = '';
> while(<FILE>)
> {
> next if /^(\s)*$/; # to skip blank lines in file
> chomp;
>
> $_=~s/\s+$//g;
>
> $sequence=$_;
> $compliment=$sequence;
> $compliment =~tr/aAtTcCgGuU/TTAAGGCCTT/;
> $rev_compliment=reverse $compliment;
>
> print "sequence : $sequence\t";
> print "rev_sequence : $rev_compliment\n";
>
> $sequence = ' ';
> $compliment=' ';
> $rev_compliment=' ';
>
> }
>
>
> And when i see the output there is some difference in the tabs in
> displays. why is that so. Any ideas
>
> sequence : TTCAAGGACTTCTATTCAGAA rev_sequence : TTCTGAATAGAAGTCCTTGAA
> sequence : TCTTGATGAAGAGGAATGGGA rev_sequence : TCCCATTCCTCTTCATCAAGA
> sequence : GCTTGGCAATCTCATGTCAAA rev_sequence : TTTGACATGAGATTGCCAAGC
> sequence : CTAGACCAATGTTTAGTTAGT rev_sequence : ACTAACTAAACATTGGTCTAG
> sequence : TAGTTGTCGTCGTATCTTTGT rev_sequence : ACAAAGATACGACGACAACTA
> sequence : GAGTAAGGCGCTTATCTTCT rev_sequence : AGAAGATAAGCGCCTTACTC
> sequence : TCTGCAACCGGAAAGGGAGC rev_sequence : GCTCCCTTTCCGGTTGCAGA
>
>
> last 2 outputs dont display my tabs why is that so.
> I checked the escape characters in the file but cant find much in them
> it look like :
> sequence : TGCAGAAGAGAGTGAGCAC^Irev_sequence : GTGCTCACTCTCTTCTGCA$
> sequence : TGCAGAAGAGAGTGAGCAC^Irev_sequence : GTGCTCACTCTCTTCTGCA$
> sequence : TGCAGAAGAGAGTGAGCAC^Irev_sequence : GTGCTCACTCTCTTCTGCA$
> sequence : CGCAGAAGAGAGTGAGCACA^Irev_sequence : TGTGCTCACTCTCTTCTGCG$
> sequence : TTGCAGAAGAAAGAGAGCAC^Irev_sequence : GTGCTCTCTTTCTTCTGCAA$
> sequence : TTGCAGAAGATAGAGAGCAC^Irev_sequence : GTGCTCTCTATCTTCTGCAA$
>
> Please advice.
>
> Thanks
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