Option to turn of gzip output

[bwlang]

trafficstars

When seqprep is used in galaxy, many downstream tools cannot handle the gzipped data (e.g. bowtie).

I'm unzipping in the wrapper for seqprep, but that's pretty dumb (zip then imediately unzip...)

would you accept a patch with an option to disable gzipped output?

[jstjohn]

Of course! Sorry for the super late response.

[eandrew]

Hello. I'm getting good results with seqprep, but am having the same difficulty as bwlang, which is slowing down my analyses quite a bit. I was wondering if anyone has made any progress in disabling the gzipped output?

[jstjohn]

Hello, I am not actively working on this. At a high level we would probably want to wrap the file IO operations in a function that optionally does gzip output. For my own selfish uses gzip io is perfect for my downstream pipelines, and I am pretty busy with other coding at the moment. Best, John

[eandrew]

Thanks for your quick response! I didn't want to try and figure something out if it had already been done.

Best,

Andy

On 09/17/2014 07:33 PM, John St. John wrote:

Hello, I am not actively working on this. At a high level we would probably want to wrap the file IO operations in a function that optionally does gzip output. For my own selfish uses gzip io is perfect for my downstream pipelines, and I am pretty busy with other coding at the moment. Best, John

— Reply to this email directly or view it on GitHub https://github.com/jstjohn/SeqPrep/issues/18#issuecomment-55930377.

E. Andrew Bennett, PhD Institut Jacques MONOD Equipe Epigénome et Paléogénome

INSTITUT JACQUES MONOD CNRS-Université Paris Diderot Bât.Buffon - 5e étage - Porte 585B 15 rue Hélène Brion 75205 PARIS CEDEX 13 - FRANCE [email protected]