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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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