DIB lab code review session, Mon 9/12 @ 3pm

[johnsolk]

I would like to share this repo with people but the code needs polishing and work. I'm not sure exactly how to tackle this issue - pydoit? - and welcome any comments and suggestions.

We'll meet in lab on Mon, 9/12 at 3pm. Please feel free to comment here too.

[ctb]

The master branch at https://github.com/ljcohen/MMETSP is the branch to look at!

[ctb]

@ljcohen is the list of scripts in the README.md (under "Automated scripts running the protocols") still accurate and up to date?

[johnsolk]

Yes, the list of 5 files are the main scripts that work right now:

1. getdata.py, download data from NCBI and organize into individual directories for each sample/accession ID
2. trim_qc.py, trim reads for quality, interleave reads
3. diginorm_mmetsp.py, normalize-by-median and filter-abund from khmer, rename, combined orphans,
4. assembly.py, runs Trinity de novo transcriptome assembly software
5. salmon.py

Added a list of other scripts to README.md. Want to to incorporate dammit.py. Haven't run this on all samples yet.

[jessicalumian]

Google doc with comments: https://docs.google.com/document/d/1vUs9gpFQfdXroqJ04JTzb4Vp3IHxXu4GAGOhrZXXjgs/edit