Skip to content

Broad XX support, performance upgrades #33

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 9 commits into from
Mar 21, 2020
Merged

Broad XX support, performance upgrades #33

Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
87a0a7e
handle broad XX codes
mmaiers-nmdp Mar 7, 2020
ac95609
relshp file
mmaiers-nmdp Mar 7, 2020
802b909
packaging
mmaiers-nmdp Mar 7, 2020
8ed549f
performance
mmaiers-nmdp Mar 8, 2020
6d72f57
performance code clinic
mmaiers-nmdp Mar 9, 2020
789d4be
gitignore and performance enhancements to pyard.py
mmaiers-nmdp Mar 10, 2020
5e914b5
validate XX codes
mmaiers-nmdp Mar 20, 2020
542d33c
Merge branch 'master' of https://github.com/nmdp-bioinformatics/py-ar…
mmaiers-nmdp Mar 20, 2020
32c72b6
minor fix to XX validation
mmaiers-nmdp Mar 20, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 3 additions & 2 deletions pyard/pyard.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -205,7 +205,7 @@ def __init__(self, dbversion: str='Latest',
locusbroad="*".join([locus,broad])
for split in dictbroad[(locus,broad)]:
locussplit="*".join([locus,split])
if locusbroad in self.xxcodes.keys():
if locusbroad in self.xxcodes:
self.xxcodes[locusbroad].extend(self.xxcodes[locussplit])
else:
self.xxcodes[locusbroad] = self.xxcodes[locussplit]
Expand Down Expand Up @@ -444,7 +444,8 @@ def redux_gl(self, glstring: str, redux_type: str) -> str:
loc_name, code = loc_allele[0], loc_allele[1]

# handle XX codes
if(ismac(glstring) and glstring.split(":")[1] == "XX"):
# test that they are valid
if(ismac(glstring) and glstring.split(":")[1] == "XX") and loc_name in self.xxcodes:
loc, n = loc_name.split("*")
return self.redux_gl("/".join(sorted(self.xxcodes[loc_name], key=functools.cmp_to_key(smart_sort_comparator))), redux_type)

Expand Down