Skip to content

Release 1.27.2 #315

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 4 commits into from
Jun 28, 2023
Merged

Release 1.27.2 #315

Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
021b22d
fixed sorting issue
Jun 28, 2023
c3ecd6b
Update ingest/author_de.py
michelle-vel Jun 28, 2023
c0dd940
Update ingest/author_de.py
michelle-vel Jun 28, 2023
7ee2f69
Merge pull request #314 from broadinstitute/mv-author-de-sorting
michelle-vel Jun 28, 2023
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
13 changes: 8 additions & 5 deletions ingest/author_de.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -92,10 +92,6 @@ def generate_result_files(self, col, genes, rest, groups, clean_val, qual):

Then final format should have type 0 type 1 in the title, and genes, logfoldchanges, qval, and mean as columns
"""
# for i in clean_val:
# val_to_sort = [i[0], i[1]]
# sorted_list = sort_comparison(val_to_sort)
# i[0], i[1] = sorted_list

names_dict = {}
all_group = []
Expand Down Expand Up @@ -153,6 +149,12 @@ def generate_result_files(self, col, genes, rest, groups, clean_val, qual):
if "rest" in i:
i = i.split("--")[0]

else:
first_group = i.split("--")[0]
second_group = i.split("--")[1]
sorted_list = sort_comparison([first_group, second_group])
i = f'{sorted_list[0]}--{sorted_list[1]}'

comparison = '--'.join([DifferentialExpression.sanitize_strings(group) for group in i.split('--')])

tsv_name = f'{self.stem}--{comparison}--{self.annot_scope}--{self.method}.tsv'
Expand Down Expand Up @@ -287,11 +289,12 @@ def check_group(names_dict, name):
def sort_comparison(ls):
"""
Naturally sort groups in a pairwise comparison; specially handle one-vs-rest
this should take in only a list of two, ex (type1 type2)
this should take in a list of groups, such as ['B cells', 'CSN1S1 macrophages']

https://en.wikipedia.org/wiki/Natural_sort_order

"""

if any(i.isdigit() for i in ls):
sorted_arr = sorted(ls, key=lambda x: int("".join([i for i in x if i.isdigit()])))
return sorted_arr
Expand Down