Python port#58
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Also defaults sisrs-python to simply wrapping sisrs
* Using python 2 for now since that what SISRS currently uses. * Add Click library for CLI parsing * Port directory setup to python
HomSap isn't matching for some reason, but it doesn't match when running normal sisrs either, so commenting out for now.
Assume commands will run as root from a CI environment such as Travis
git-core, wget, bzip2, and software-properties-common installed in before_install.sh now rather than relying on the base system having them.
Wrote a script for comparing bams. Was using bamHash before, but it only compares read names and sequences, not mappings. Also uncommented the output alignment test
This is for the transition to python 3, since apparently the hash algorithm changed which makes the default ordering of dictionaries different. Also switched bin/sisrs to point to sisrs/filter_nexus_for_missing.py so we're not using two different ones.
In general this required sorted dicts in order to create deterministic ordering, since Python's hash algorithm for internal representation of dicts apparently changed from Python 2 to Python 3.
My previous couple commits weren't having any effect because I wasn't rebuilding the docker image
Broken commit.
Currently only bowtie2 is implemented
Last commit broke it
We didn't really need all the features and click has some issues with Python 3 for now.
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@anderspitman could you submit this pull request to the python port branch. Let's leave master with bash for now. |
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@BobLiterman this PR represents a good jumping off point for moving everything over to Python. I finally got all the Python 3 stuff working.
In order to generate test data that I could use to verify the changes here, I needed to make a few modifications to bash SISRS. Those are represented in #57. That PR does not strictly need to be merged, but I wanted to make sure it was obvious what needed to change in order to compare a bash SISRS + Python 2 run against a sisrs-python + Python 3 run (this PR).