File::Wrap and Fasta format

Wrap sequences for widely used Fasta format, without the hassle of installing BioPerl and learning to use Bio::SeqIO or rolling your own sub. Not difficult other than being so obvious; a true kick-yourself.

use Text::Wrap;
$Text::Wrap::columns = 51; #includes terminal \n

...

print $fh ">$description\n";
print $fh wrap('', '', $sequence_string."\n");
[download]

Comment on File::Wrap and Fasta format Download Code

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Re: File::Wrap and Fasta format by aging acolyte (Pilgrim) on Mar 13, 2003 at 12:21 UTC
I have always liked a simple regex to format for fasta for 80 nt per line: `$seq =~ s/([^\n]{80}\|[^\n]{1,79}$)/$1\n/g; print $out ">$description\n$seq"; close $out;` [download] A.A.	[reply] [d/l]
Re: File::Wrap and Fasta format by robsv (Curate) on Mar 25, 2003 at 21:41 UTC
Here's another shorter regex (although it's not doing any substitution): `... print $fh ">$description\n"; print $fh "$_\n" foreach ($seq =~ /.{1,50}/g); ...` [download] The fastest way I've found of dumping a FASTA sequence (with very large sequences, anyways), is with `substr`: `... print $fh ">$description\n"; print $fh substr($seq,0,50,'') . "\n" while ($seq); ...` [download] The thing to watch here is that it's destructive - `$seq` will be empty when it finishes. - robsv	[reply] [d/l] [select]