[Bioperl-l] How to read in FASTA formatted sequence without
golharam at umdnj.edu
Fri Sep 30 19:16:42 EDT 2005
True. Ok, so I have a raw sequence instead of fasta...when I try to
read in the sequence using raw format, it only reads in the first line.
I'm thinking of modifying the raw module and making a multilineraw
module that will stop reading on a newline or EOF.
I don't want to modify the actual files because they might screw up all
my other scripts. I could write one to insert the fasta header in a tmp
file then concatente the sequence to the file, but it just doesn't seem
like a clean solution to me.
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Richard
Sent: Friday, September 30, 2005 5:59 PM
To: golharam at umdnj.edu
Cc: 'Bioperl List'
Subject: Re: [Bioperl-l] How to read in FASTA formatted sequence without
Well, maybe I am mistaken, but isn't the header line the item that
makes a FASTA file a FASTA file?
As in, now you have a raw sequence.
On Sep 30, 2005, at 3:43 PM, Ryan Golhar wrote:
> I'm looking for the easier way to read in a fasta file that doesn't
> contain the fasta header, ie the ">..." line.
> I tried just specifying fasta, but then the first line of the sequence
> is taken as the name of the sequence. I also tried specifying raw,
> then only the first line is read.
> Is there any (easy) way to do this without reformatting the fasta file
> or creating a new one? Thanks,
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