ctb/khmer — pull request #23 by fomightez (2013-07-28 20:48:59+00:00)
Title: fixing and supplementing some handling of fastq entries

Hi Titus,
When I was using khmer from ami-d6e581bf, I noticed two things that I have addressed on this branch.
1) fasta-to-fastq.py didn't do what I expected it to do based on the name and what fastq-to-fasta.py did. I addressed that by changing that file.
2) And I wanted to be able to do what remove-N.py does but do it with reads still in fastq form, and so I made remove-Nfq.py. I did this based on quality-trim.py and found it worked much more efficiently on files with a lot of reads than when I initially based it on remove-N.py.

(I really like that you pre-installed a lot of stuff on that ami-d6e581bf. Made my life much easier. http://ged.msu.edu/angus/2013-04-assembly-workshop/installing-software.html)

Thanks,
Wayne

Below is the actual commit message from my branch:

Addressing deficiencies in handling of files that are lists of fastq
entries. Specifically, addressed fasta-to-fastq.py converter and added
a script that will perform the remove-N tasks for files of fastq entries.

- because I wanted to convert the output of strip-and-split-for-assembly.py
back to fastq for a certain step workflow, I noticed fasta-to-fastq.py
did not function as I expected

- remove-Nfq.py does what remove-N.py does but does it with fastq reads.
This was initally based on remove-N.py but I noticed inefficiencies and
so reworked it based on quality-trim.py and it runs way more
efficiently.