Double RegEx

MonkPaul has asked for the wisdom of the Perl Monks concerning the following question:

Hello Monkies,

I have a question - Can i use a second regex when looking through a line in a file.

For instance i am currently looking for Homo sapien in one line of a file, but i also want to look for chromosome 11 say. At the moment, i am saving the filtered data from Homo sapiens search into an array, then conducting the search on this to find the chromosome 11.

  for (my $i = 0 ; $i<scalar @line; $i++)
  {
     if ($line[$i] =~ /^>/)
     {
           $current_subject = $line[$i];
          chomp ($current_subject);
          push (@filtered_subjects, $current_subject);
     }
  }
  my @element;
[download]

So stored in the array is:

>gi|14670349|ref|NM_032999.1| Homo sapiens general transcription facto
+r II, i (GTF2I), transcript
>gi|2827179|gb|AF035737.1|AF035737 Homo sapiens general transcription 
+factor 2-I (GTF2I) mRNA, complete
>gi|19908489|gb|AF343351.1| Mus musculus TFII-I repeat domain-containi
+ng protein 3 beta 7 mRNA,
[download]

Then i look through each element looking for the species, which comes from a HTML list.

  foreach my $z (@filtered_subjects)
  {
     chomp $z;
     @element = split('\|', $z);
     if($element[4] =~ /\Q$Homosapiens\E/)
     {
     push(@chromoLine, $z);
     }
  }
}
[download]

Is this the best way to do it, or can i use something like:

     if($element[4] =~ /\Q$Homosapiens$choromosome\E/)
[download]

Any help is appreciated.

thanks,
MonkPaul.

Comment on Double RegEx Select or Download Code

Replies are listed 'Best First'.
Re: Double RegEx by ikegami (Patriarch) on Jun 27, 2005 at 14:38 UTC
If you know the order in which they'll appear in the string being matched, `if($element[4] =~ /\Q$Homosapiens\E.\Q$choromosome\E/)` will work fine. If you don't know the order, you want `if ($element[4] =~ /^ (?=.?\Q$Homosapiens\E) (?=.?\Q$choromosome\E) /x)` [download] It reads: "Match homo sapiens somewhere after the start of the line, then match chromosome somewhere after the start of the line." Update*: I overlooked the obvious: `if ($element[4] =~ /\Q$Homosapiens\E/ && $element[4] =~ /\Q$choromosome\E/)` [download] And since you're searching for constant strings, the following would be even faster: `if (index($element[4], $Homosapiens) >= 0 && index($element[4], $choromosome) >= 0)` [download]	[reply] [d/l] [select]
Re: Double RegEx by MonkPaul (Friar) on Jun 27, 2005 at 14:44 UTC
Excellent Thas what i needed. I was not sure if people would get what i needed. I will just run this in my looping system and see if blast-off occurs. Will keep you posted. cheers.	[reply]
Re: Double RegEx by MonkPaul (Friar) on Jun 29, 2005 at 13:27 UTC
One other problem i have just found - At the moment its finding "chromosome 2" where the represents any other number. How can i complete this so it only looks for chromosome 2 only and say not 20. MonkPaul.	[reply]
Re^2: Double RegEx by ikegami (Patriarch) on Jun 29, 2005 at 14:42 UTC
`/chromosome 2(?!\d)/` [download] "chromosome 2", not followed by a digit.	[reply] [d/l]
Re: Double RegEx by rev_1318 (Chaplain) on Jun 27, 2005 at 14:38 UTC
Where do you use the 'Double RegEx'? Currently, your entire code could be rewritten as: `chomp @lines; foreach (@lines) { next unless /^>/; push @chromoLine, $_ if (split /\\|/)[4] =~ /\Q$Homosapiens\E/; }` [download] Paul	[reply] [d/l]