YeoLab / outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
http://yeolab.github.io/outrigger/
BSD 3-Clause "New" or "Revised" License
61 stars 22 forks source link

Low memory #57

Closed olgabot closed 7 years ago

olgabot commented 7 years ago

In running outrigger psi or other command line programs, I get these errors:

/home/obotvinnik/workspace-git/outrigger/outrigger/commandline.py:937: DtypeWarning: Columns (18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,42,43,44,45,46,47,48,49,50,51) have mixed types. Specify dtype option on import or set low_memory=False.
  cl = CommandLine(sys.argv[1:])

Since I expect most users of outrigger to use it on a large dataset, on a supercomputer, this PR sets low_memory=False by default, but can be turned off with the command line flag --low-memory

willingc commented 7 years ago

@olgabot I did a quick code review on this. It looks good to me.

olgabot commented 7 years ago

Yep, just gotta add some release notes and maybe a test.