Hi Anjan,
Not able to get where your "column" is. I am Assuming your column is
in Text file. However even if it is not in text file, then also this may
provide you a fair hint about how to proceed further.
use warnings;
use strict;
open FH,"example.txt" or die "Cannot open file: $!"; #(example.txt is file
containing your column)
undef $/;
my $text = <FH>;
$text=~s/[^AGTC]//g; #remove anything which is not A,G,T or C
print "$text"; # $text will contain your required output
Let me know if this helps.
Thanks
Sanket Vaidya
-----Original Message-----
From: ANJAN PURKAYASTHA [mailto:[EMAIL PROTECTED]
Sent: Tuesday, September 23, 2008 6:52 AM
To: beginners@perl.org
Subject: pattern matching question
here is my problem:
i have to check the entries of a column and write them out to a file if they
happen to be DNA sequences ie they are exclusively composed of the letters
A, T, G, C- no spaces or digits.
the column also happens to have other strings that are made of
word/digit/space characters.
i tried
if($x=~ /[ATGC]/ )then .....
however this pattern matching expression is unable to filter out the non-DNA
sequences.
i have also tried other expressions too convoluted to write out here.
any ideas?
tia,
anjan
--
=============================
anjan purkayastha, phd
bioinformatics analyst
whitehead institute for biomedical research
nine cambridge center
cambridge, ma 02142
purkayas [at] wi [dot] mit [dot] edu
703.740.6939
http://www.patni.com
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