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matsengrp / cft

Clonal family tree
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process_partis.py - small bug? #243

Closed dunleavy005 closed 6 years ago

dunleavy005 commented 6 years ago

Hi,

In process_partis.py, line 41 default_germline_sets = os.path.join(partis_path, '/data/germlines/human') isn't doing what it's supposed to be doing. It always outputs /data/germlines/human, I did some tinkering and found that the line should be default_germline_sets = os.path.join(partis_path, 'data/germlines/human') with no front-facing blackslash. Can someone confirm this please (or at least be willing to make the change on master branch)?

metasoarous commented 6 years ago

If you run with PARTIS=/your/partis/install/path ./process_partis.py ..., it should work.

metasoarous commented 6 years ago

That having been said, it should/could be data/... instead of /data/....

dunleavy005 commented 6 years ago

So I originally ran this using your error message, like:

export PARTIS=$PWD/partis
bin/process_partis.py .....

and this definitely did not work. I did some experimenting with os.path.join and I found anytime I took off the front-slash from the 2nd path to be joined, the two paths would merge, otherwise not. I realized I probably won't need to use default germline files so its a moot point, but it seems as it is default germline file paths aren't properly joining (unless I'm missing something in my setup).

metasoarous commented 6 years ago

So it is! Good catch.