no automatic line wrap on fasta

[Former user]

i'm pushing my luck here , but that automatic line wrap drives me to drink.

[Jason Vander Heiden]

Heh. It irks me too and it's actually already on my todo list.

Instead of using Bio.SeqIO for FASTA/FASTQ writing, instead:
Write function to return a writer class based on the output type.
Use Bio.SeqIO.FastaIO(handle, wrap=None) for FASTA output.
Use Bio.SeqIO.QualityIO.FastqPhredWriter for FASTQ output.

As a workaround:

> seqmagick mogrify --line-wrap 0 input.fasta

http://fhcrc.github.io/seqmagick/

[Former user]

thanks, I seqmagick do you seqtk? seqtk is blazingly fast.

Sonia Timberlake, PhD Senior Data Scientist, AbVitro, Inc. 27 Drydock Ave, Boston [e-mail] We're hiring! Visit abvitro.com

[Jason Vander Heiden]

Nope. Seqmagick is my favorite little sequence munging toolkit. It's not overly fast though. I'll check out seqtk.

[Former user]

functionality not as broad and documentation not always native english but Heng Li sure knows how to make things fast.

Sonia Timberlake, PhD Senior Data Scientist, AbVitro, Inc. 27 Drydock Ave, Boston [e-mail] We're hiring! Visit abvitro.com

[Jason Vander Heiden]

Seeing as we might need to redo the entire I/O interface for performance reason, I'm going to close this. We should still do it, but in the new interface instead of dedicating effort to the old one.