Hi, I'm new in perl and would be intrested to have suggestion from experienced people on how to write optimized code for the following task:
I work with genomic data filesize higher than 1Go and have 2 files with lines that looks like this:
** A line from file1:
HWI-EA332_91026_1_1_7_586#TCTTAT/1 + Chr3 67121130 TATTNTAAGTCTATGTTGGGGGGGTGGTCATTGAATGTAAGNTGGGTCTC
** A matching line from file2:
HWI-EA332_91026_1_1_7_586#ACATAA/2 - Chr7 127074854 AAAATAAAGCTNATCTGGAAGCAACAGTANGAAGCAGAAGACTGNACACC
The id is the subsring EA332_91026_1_1_6_683 identified by  my @token = split('\-|\#', $line);
What i want to do is:
for each id in file 1 look if same id exist in file 2 and when there's a match:
* I add the matching line from file 1 followed by the matching line from file 2 to a new file (matched_pair)
* based on a tab delimited split of the line take column 2/3 from the matching line in file1 and file2 and the absolute value of the difference between column 4 in file1/file2 (gap_dist) and the id.
Based on the example above we expect to have this line :
EA332_91026_1_1_7_586 + Chr3 - Chr7 59953724
Thanks in advance for your kind help.
Regards,
Ramzi

In reply to generating merged data from matching id in 2 files by ramouz87

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