File::Wrap and Fasta format

[clairudjinn]

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");

[aging acolyte]

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;

A.A.

[robsv]

Here's another shorter regex (although it's not doing any substitution):

...
print $fh ">$description\n";
print $fh "$_\n" foreach ($seq =~ /.{1,50}/g);
...


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);
...

The thing to watch here is that it's destructive - $seq will be empty when it finishes.

- robsv