riya
New User
Oct 26, 2009, 4:50 PM
Post #1 of 1
(1329 views)
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am a perl beginner and need some help with regex
Input for this code is :
aatgatgataaggtaaggtatgatgatgatgatgatagtagannnnnnnnnatgcatga'/atgca.atgactagca/atgactagcaaggtaaggtaaggtaaggtaaggtatgatgatgannnn./atgatgactagactgacaaggtaaggtaaggtatgatgatgatcgatgacgat... and so on
Here i am trying to assign input file as a scalar variable and trying to find a match of "aaggtaaggt" and then skip some 100 characters whether they are alphabets or symbols or any wildcard characters after skipping exact 100 characters, i am again asking code to start search for match again and every time it finds a match , i am counting and asking to print..
As of my knowledge i have tried using substr of match as pos1 and had set offset for 100 and then assigned that as initial pos for reading second match , but failed to get the correct output, then tried here post match as $' but doubt whether it is correct or not.
#!/usr/bin/perl
$count1 = 0;
open (FILE, "INPUT") || die "cannot open $!\n";
while ($line = <FILE>){
if(($line=~m/(aaggt){2}/ig)&&($'=~m/([atgcn]{100,})/i)) {
$count1 ++ ;
print " " ,$1, "\t";
print "count1 \t " ,$count1 , "\n" ;
}
}
Please, help me figuring out this task. Thanks
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