[EMBOSS] fasta single-line sequence format?

Fields, Christopher J cjfields at illinois.edu
Tue Aug 27 16:29:32 UTC 2013

On Aug 27, 2013, at 9:51 AM, Peter Cock <p.j.a.cock at googlemail.com>

> On Tue, Aug 27, 2013 at 3:08 PM, Fields, Christopher J
> <cjfields at illinois.edu> wrote:
>> Is there a name for the FASTQ analog?  Maybe 'unwrapped'? :)
> No, EMBOSS always write unwrapped FASTQ on output,
> but accepts line wrapped FASTQ on input.
>> Neils: Re: 'Most genome packages use it': can you specify?
>> Most genome packages I know allow the flexibility to use
>> standard line-wrapped FASTA as well, so coding an indexing
>> scheme for a non-standard FASTA alone seems… tricky.
>> Unless you intend on allowing both, and 'unwrapped' is just
>> for optimization.
>> chris f.
> e.g. faidx by Heng Li allows line wrapped FASTA, with the
> proviso that each record uses the same line wrapping length
> (so it can't cope with arbitrary FASTA files).
> Peter

Yes, this is the same reasoning for Lincoln's Bio::DB::Fasta in bioperl.


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