So, you have a "locus" file containing lines with 6 tab-delimited fields (and maybe some lines that don't fit that description), and you have a "molecules" file with a list of target strings, and your goal is to print the 6-field "locus" lines that contain any of the "molecule" strings in the first or second field.

If I got that right, then I think something like the following will do: 

open( MOL, "molecules" );
@molecules = <MOL>;
close MOL;
map { chomp; $_ = quotemeta; } @molecules;

$bigRegex = join '|', @molecules;

open( LOCUS, "locus" );
@locus = <LOCUS>;
close LOCUS;

foreach (@locus) {
    print if ( scalar( split /\t/ ) == 6 &&
               /^([^\t]+\t)?($bigRegex)/ );
}

[download]
You may want to look at "qr" on the perlop manpage (under "Regexp Quote-like Operators), if you have a lot of molecule patterns to look for and/or a lot of locus data to go through. The "print if" condition says that there must be 6 fields on the line, and the set of molecule strings in $bigRegex needs to match either at the beginning of each line, or after the first tab character.

In reply to Re: Parsing a tab delimited file by graff
in thread Parsing a tab delimited file by snowy

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