hi all, the "column" is in a text file. fyi, david's pattern matching expression (/^[ATGC]+$/i) did the job perfectly. thanks all for you feedback! anjan
On Tue, Sep 23, 2008 at 5:07 AM, sanket vaidya <[EMAIL PROTECTED]>wrote: > > > > 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 > World-Wide Partnerships. World-Class Solutions. > _____________________________________________________________________ > > This e-mail message may contain proprietary, confidential or legally > privileged information for the sole use of the person or entity to whom this > message was originally addressed. Any review, e-transmission dissemination > or other use of or taking of any action in reliance upon this information by > persons or entities other than the intended recipient is prohibited. If you > have received this e-mail in error kindly delete this e-mail from your > records. If it appears that this mail has been forwarded to you without > proper authority, please notify us immediately at [EMAIL PROTECTED] and > delete this mail. > _____________________________________________________________________ > -- ============================= 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
