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Re: character-by-character in a huge file

by Itatsumaki (Friar)
on Apr 08, 2004 at 20:48 UTC ( #343750=note: print w/replies, xml ) Need Help??

in reply to character-by-character in a huge file

This is a fasta-formatted sequence file, right? You're best bet for doing this is might be the BioPerl library. They have both a regular fasta-parser as well as a special indexed parser for genome-sized files. The latter works really well if you need to get subsequences from a file. For instance, I use the indexed-version when I want to extract all mRNA sequences from a single chromosome.

Here is the code for using the indexed-version. It processes every mRNA on every chromosome in a typical eukaryotic genome in about 30 minutes on a P4.

# set up chromosome sequence object my $file = $chromosome.'.fa'; my $seqio = Bio::SeqIO->new( -format => 'largefasta', -file => $file ); # set up range parameters my $strand = '+'; my $seq_start = 1_000_000; my $seq_end = 2_000_000; my $downstream= 10_000; # handle sequences on both strands if ($strand eq '+') { $seq_start = $tx_start - $upstream; $seq_end = $tx_start + $downstream; if ($seq_start < 0) { next(); } if ($seq_end > $length) { next(); } $seq_mRNA = $seq_chr->trunc($seq_start,$seq_end); } elsif ($strand eq '-') { $seq_start = $tx_end + $upstream; $seq_end = $tx_end - $downstream; if ($seq_end < 0) { next(); } if ($seq_start > $length) { next(); } $seq_mRNA = $seq_chr->trunc($seq_end,$seq_start)->revcom(); } else { warn "No strand: $strand!\n"; next(); } # write seq to a file my $outfile = $mRNA.'.fasta'; open(OUT, '>', $outfile); print OUT ">$mRNA\n", $seq_mRNA->seq(); close(OUT);

And there are always the usual caveats with BioPerl -- great user support group, fairly big initial learning curve, highly object-oriented library....


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