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Re: add letters to the begin of the sentence

by Kenosis (Priest)
on Sep 12, 2013 at 17:56 UTC ( #1053777=note: print w/replies, xml ) Need Help??

in reply to add letters to the begin of the sentence

Since you're working with fasta files, consider becoming familiar with Bio::SeqIO--a module that's a powerful tool for working with fasta and other such formats.

For example, to achieve your desired results using the module, you can do the following:

use strict; use warnings; use Bio::SeqIO; my $in = Bio::SeqIO->new( -file => 'file1.fasta', -format => 'Fasta' + ); my $out = Bio::SeqIO->new( -file => '>file2.fasta', -format => 'Fasta' + ); while ( my $seq = $in->next_seq() ) { my $newSeq = Bio::Seq->new( -display_id => $seq->id, -seq => 'aaaa' . $seq->seq ); $out->write_seq($newSeq); }

Output results:

>dddd aaaaabcdef >eeee aaaabcdef

Notice that the module permits you to access sequences and ids as objects, using the "->" notation. For example, in the above, we prepend "aaaa" to the original sequence by doing the following:

'aaaa' . $seq->seq

Then, create a new object with the modified sequence that's written to a new file.

The module offers many more options for working with fasta (and other similarly formatted) files.

Hope this helps!

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[perldigious]: Mine too thezip, especially my German Shepherd. He looks like he is about to die of heat exhaustion all summer, so he goes nuts when winter comes and he can play in the snow.
[stevieb]: my main off-road vehicle nowadays is a strengthened mercedes ML320. I'm very hard on it, but I've never had any real issues at all (I love how small and light it is, and it has a very, very good centre of gravity for how I roll)
[perldigious]: "for how I roll"... ahhh, I see what you did there stevieb.

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