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    <p>I lifted Borodin's process_seq function but used Bio:SeqIO to read in the file sequence by sequence, an advantage over manually reading line by line and the logic to determine various processing. I believe those advantages are:</p> <ul> <li>Code that has been developed and tested by many others</li> <li>Whenever possible, if output is done via the Bio::SeqIO module, the result file can then be read using Bio::SeqIO read (<code>next_seq</code>) method.</li> <li>Other reasons I can't think of now :-)</li> </ul> <p>I imagine the BioPerl package of Bio Genetic code modules must be overwhelming to a biologist beginning programming. He might not be willing to try to dig out the information he needs to begin building a program. <a href="http://www.bioperl.org/wiki/Main_Page" rel="nofollow">BioPerl wiki</a> is a good starting place, especially the Howto section, and then there's a how to for beginners and others. You'll find code examples which are mostly(?) helpful. <a href="http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/Seq.pm" rel="nofollow">Bio::Seq</a> has some good code examples in the beginning and is where most of the general sequence functions are. Also, for input/output, the <a href="http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/SeqIO.pm" rel="nofollow">Bio::SeqIO</a> module is used and it has examples at the beginning of it's manual.</p> <pre><code>#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; my $gpat = '[G]{3,5}'; my $npat = '[A-Z]{1,25}'; my $pattern = $gpat.$npat.$gpat.$npat.$gpat.$npat.$gpat; my $regex = qr/$pattern/i; my $in = Bio::SeqIO-&gt;new ( -file =&gt; "fasta_dat.txt", -format =&gt; 'fasta'); my @totals; while ( my $seq = $in-&gt;next_seq() ) { process($seq); } print "Totals: "; print "@totals\n"; sub process { my $seq = shift; my @offset = map {sprintf '%.0f', $seq-&gt;length * $_ / 3} 1..3; my $sequence = $seq-&gt;seq; my @count = (0,0,0); while ($sequence =~ /$regex/g) { my $place = $-[0]; for my $i (0 .. 2) { next if $place &gt;= $offset[$i]; $count[$i]++; last; } } print $seq-&gt;id, "\n@count\n"; $totals[$_] += $count[$_] for 0 .. $#count; } </code></pre>
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    1. USChris Charley
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    1. COHello Chris and many thanks for your answer! Indeed I am absolutely new to programming and Perl. I am actually interning in bioinformatics for 2 months and was referred to "Beginning Perl for Bioinformatics". The scope of the book however does not cover problems like these. So yes, not only are many of the variables and functions new, the use of BioPerl module is also unfamiliar. It makes me realize how amazing Perl and programming is and how much I have yet to learn...perhaps 2 months is not sufficient. I am learning something new everyday!
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    2. COYou can also search this site or [http://perlmonks.com/?node=Super%20Search] at Perl Monks. Search for 'fasta' or 'Bio::SeqIO'.
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    3. COMany many thanks Chris! :)
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