Is there a name for the FASTQ analog? Maybe 'unwrapped'? :) 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. On Aug 27, 2013, at 8:44 AM, Peter Rice <ricepet...@yahoo.co.uk> wrote: > Suggestions please for a format name to describe fasta format with the > sequence always on a single line > > (needed for output only - it will be valid as format 'fasta' for input). > > Peter Rice > EMBOSS Team > > On 27/08/2013 11:03, Niels Larsen wrote: >> Yes, i meant both input and output. It would not be default, so >> hopefully no programs should get a long-line surprise. The speed >> advantage is a single read for the whole sequence and not having >> to remove newlines. Indexing sub-sequences with locators >> becomes straightforward, the newlines don't get in the way. Most >> genome packages use it, i think, including mine. Thanks, yes i >> thought it must be quite easy to do .. >> >> Niels >> >> On Tue, 2013-08-27 at 10:41 +0100, Peter Rice wrote: >>> On 27/08/2013 09:40, Niels Larsen wrote: >>>> EMBOSS list, >>>> >>>> I could not find a fasta single-line sequence format, is it >>>> missing? having the sequence as a single line does not >>>> violate fasta format i think, and many programs use it >>>> because of speed and indexing convenience. >>> >>> You mean as an output format I assume? (it would be no problem for input). >>> >>> Easy to implement, but needs a name so you can so specify >>> -osformat fastasingle (for example) >>> >>> It can also be an issue for applications that fail to check for very >>> long input lines. >>> >>> I don't see any real benefit for indexing - you only need to point to >>> the start of the ID line for that. Maybe there are applications that map >>> the sequence string and want to have no extra characters. >>> >>> regards, >>> >>> Peter Rice >>> EMBOSS Team >>> >> > > _______________________________________________ > EMBOSS mailing list > EMBOSS@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss