Hi all.

I am attempting to extract the Name and Nucleotide Sequence information from a file which has the following format: 

GeneID: 1002
Name: cadherin 4, type 1, R-cadherin (retinal)
Chromo: 20
Cytoband: 20q13.3
Nucleotide Sequence: atgaccgcgggcgccggcgtgctccttctgctgctctcg
acagcgagactggagatatcgtcacagtggcggctggcctggaccgagagaaagttcagc
cagcttgcgcatcctgtacctggaggccgggatgtatgacgtccccatcatcgtcacaga

[download]


The code I wrote to accomplish this seemingly simple task is below: 

#!/usr/bin/perl -w
use strict;
use autodie;

open FH, '<', 'test.dat';
    my @data = <FH>;
close FH;

open FH2, '>', 'seq.dat';

for (@data)
{
    if (/Name:\s(.*?).*Nucleotide\sSequence:\s(.*?)/xms)
    {
        print FH2 $1, $2, "\n\n";
    }
}

close FH2;

[download]


Ideally, the output file will consist of a collection of two rows in the following format (where 'blah' is the name and 'foo' is the sequence):

blah
foo

blah
foo

...

Thanks for the help.

In reply to Extracting multiple rows in a text file with a regex. by Anonymous Monk

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