Ad:

Perl Discussion Thread
Unsolved
Views: 1450

Oct 28th, 2009

Perl regex

Expand Post »

I 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

Similar Threads

Perl Regex help in Perl
Perl Regex to VB Regex VS 2008 in VB.NET
Confounding Regular Expression Problem in Perl
add text in the c functions.plz help me in Perl
Extrace Pattern(E-mail ID) from text file in Perl

riya0707

Reputation Points: 10

Solved Threads: 0

Newbie Poster

Offline

2 posts
since Oct 2009

Permalink

Oct 28th, 2009

Re: Perl regex

Perl Syntax (Toggle Plain Text)
#!/usr/bin/perl -w
 
use strict;
 
undef $/;	# Input Record separator
 
open (FILE, "INPUT") || die "cannot open $!\n"; 
my $var=<FILE>;  # Assign the file handler to scalar variable
close (FILE);
 
my $match=qq{aaggtaaggt};  # Declare your text
my $count=0;
 
# ($match)  -> aaggtaaggt
# (.{100})? -> any 100 character match o or 1 times
 
$count++ while ($var=~ m{($match)(.{100})?}gs);
 
print "\nAs per rule text '$match' find $count times";
#!/usr/bin/perl -w

use strict;

undef $/;	# Input Record separator

open (FILE, "INPUT") || die "cannot open $!\n"; 
my $var=<FILE>;  # Assign the file handler to scalar variable
close (FILE);

my $match=qq{aaggtaaggt};  # Declare your text
my $count=0;

# ($match)  -> aaggtaaggt
# (.{100})? -> any 100 character match o or 1 times

$count++ while ($var=~ m{($match)(.{100})?}gs);

print "\nAs per rule text '$match' find $count times";

k_manimuthu

Reputation Points: 55

Solved Threads: 24

Junior Poster in Training

Offline

93 posts
since Jun 2009

Permalink

Oct 29th, 2009

Re: Perl regex

Hi @k_manimuthu Thanks for the reply ur clear way of explaining the code was helpful and i figured it out.

Last edited by riya0707; Oct 29th, 2009 at 9:08 pm.

riya0707

Reputation Points: 10

Solved Threads: 0

Newbie Poster

Offline

2 posts
since Oct 2009

Permalink

Oct 31st, 2009

How to convert string to an expression in PERL

I have a quesion for my problem with using mysql and perl programming.

- data from mysql is logic expression. After query I get it's value on string format:

my $data = "$sex < 1 && $age >= 17 && $age <= 40 && ',1,2,3,' =~m/(,)$optid(,)/";

In this expression $sex,$age,$optid is variables

- How to make Perl understanding this function?
my $sex,$age,$optid;
if ($data) {
........
........
}

as

if ($sex < 1 && $age >= 17 && $age <= 40 && ',1,2,3,' =~m/(,)$optid(,)/) {
........
........
}

Please!!!!

thangdd

Reputation Points: 10

Solved Threads: 0

Newbie Poster

Offline

2 posts
since Oct 2009

Permalink

Oct 31st, 2009

Re: Perl regex

Quote ...

I have a quesion for my problem with using mysql and perl programming.

I think that is a good question but to avoid confusion please start a new thread for it, instead of posting it as a reply to this thread's question.

d5e5

Reputation Points: 153

Solved Threads: 142

Master Poster

Offline

740 posts
since Sep 2009

Permalink

Nov 3rd, 2009

How to convert string to an expression in PERL

Click to Expand / Collapse Quote originally posted by d5e5 ...

I think that is a good question but to avoid confusion please start a new thread for it, instead of posting it as a reply to this thread's question.

thank, I've solved my problem. By using eval function

thangdd

Reputation Points: 10

Solved Threads: 0

Newbie Poster

Offline

2 posts
since Oct 2009

This thread is more than three months old

No one has posted to this discussion for at least three months. Please let old threads die and do not reply to them unless you feel you have something new and valuable to contribute that absolutely must be added to make the discussion complete. Otherwise, please start a new thread in this forum instead.

Previous Thread in Perl Forum Timeline: Issue with Cron and Perl Script Variables

Next Thread in Perl Forum Timeline: [PROBLEM] inverting a list

DaniWeb Message

Cancel Changes

User Name
Password