Add option to write FASTA sequence with a configurable number of bases per line or as a single line

simon-anders / htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

https://htseq.readthedocs.io/en/release_0.11.1/

GNU General Public License v3.0

122 stars 77 forks source link

Add option to write FASTA sequence with a configurable number of bases per line or as a single line #10

Closed unode closed 7 years ago

unode commented 7 years ago

In large FASTA files the newline breaks add a significant overhead to the file. This option allows outputting the sequence in a single line instead of 70 character blocks.

iosonofabio commented 7 years ago

Thanks @Unode! I see the utility of this, but would prefer an option like break_sequence_line_every=70 that allow the uer to choose how long lines she wants to have. You think you can get around to doing that?

Thanks

unode commented 7 years ago

Done. I'd also add a small unittest but I can't find a test framework in the repository so leaving as-is.

EDIT: Rebased on current master

iosonofabio commented 7 years ago

@unode Thanks also for rebasing. A few comments:

unit test does not really exist (sigh!) but there are doctests in the doc/*.rst files. In any case, we are not starting a unit test suite with this PR ;-)
I don't like the word bases, because the sequence could be any characters. Could you please rephrase?
Could you please add a docstring that explains the option?

Thanks!