[Bioperl-l] Sequence matching problem!

Kurt Gobain enrique_rulz at yahoo.com
Sat Feb 24 16:23:59 EST 2007



Heikki Lehvaslaiho wrote:
> 
> Kurt,
> 
> There are  few things in your code to note:
> 
> - regexp /C*T/ matches any T preceded by zero or more Cs,
>   not what you meant
> - $- and $+ are among the "expensive" perl functions worth 
>   not using unless you have to. Using them once in your 
>   code slows execution down considerable. There is always 
>   an other way.
> - Keep in mind what you want to use the match positions for: 
>   Human readable locations usually start counting with 1 but
>   perl code uses 0 as the first location. The code below assumes
>   you want to print the locations out.
> 
> Study my example code below.
> 
> Yours,
> 	-Heikki
> 
> ###################################################################
> #!/usr/bin/perl
> $seq = "GATCAAT";
> #$pattern=  'C*T';
> $pattern=  'C.*T';
> 
> while ($seq =~ m/($pattern)/gi) {
> 
>     $match = $1;
>     $end = pos($seq);
>     $start = $end - length($match) +1;
> 
>     print "$match : $start - $end\n";
> }
> 
> ###################################################################
> 
> 



Thanx for the instant reply!...Sorry cudn reply earlier..

Code works perfectly fine...but...sum time its not givin reqd o/p..For eg.
If I type sequence as "GATCAAGTCAGGAT" & pattern to be matched as T.*A..then
o/p which I am getting frm above prog is TCAAGTCAGGA instead of TCA...
& 1 more thing Is there n e chance by which I can replace T*A to T.*A cos
the code which I need to write says T*A shod be only the input not T.*A..So
Can we use replacment reg ex...sumthing like 
$pattern =~  s/.*/*/...or sumthing else...
But its kinda givin sum error again...Dam! Regex is really hairy!!...:P

N e ways thanx a lot again for the code...Hope to listen frm you soon!

Kurt!


-- 
View this message in context: http://www.nabble.com/Sequence-matching-problem%21-tf3275153.html#a9137941
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



More information about the Bioperl-l mailing list