Skip to content
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

Update MCF Wrapper Code #144

Open
wants to merge 6 commits into
base: master
Choose a base branch
from
Open

Update MCF Wrapper Code #144

Changes from 1 commit
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
32bd0e6
update mcf wrapper code
ntalluri Jan 24, 2024
a9d6869
update SPRAS mcf to use versioned image
ntalluri Jun 24, 2024
dfd2e14
Merge branch 'master' into update_mcf
agitter Jun 24, 2024
e46ce1f
Merge master branch
agitter Feb 28, 2025
d41ab32
updated comment
ntalluri Mar 3, 2025
9a4ccae
pre-commit
ntalluri Mar 3, 2025
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
10 changes: 2 additions & 8 deletions spras/mincostflow.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -53,11 +53,8 @@ def generate_inputs(data, filename_map):
# create the network of edges
edges = data.get_interactome()

# Format network edges
edges = convert_undirected_to_directed(edges)

# creates the edges files that contains the head and tail nodes and the weights after them
edges.to_csv(filename_map['edges'], sep='\t', index=False, columns=["Interactor1", "Interactor2", "Weight"],
edges.to_csv(filename_map['edges'], sep='\t', index=False, columns=["Interactor1", "Interactor2", "Weight", "Direction"],
header=False)

@staticmethod
Expand Down Expand Up @@ -152,8 +149,5 @@ def parse_output(raw_pathway_file, standardized_pathway_file):

df = pd.read_csv(raw_pathway_file, sep='\t', header=None)
df = add_rank_column(df)
# TODO update MinCostFlow version to support mixed graphs
# Currently directed edges in the input will be converted to undirected edges in the output
df = reinsert_direction_col_undirected(df)
df.to_csv(standardized_pathway_file, header=False, index=False, sep='\t')
df.to_csv(standardized_pathway_file, header=True, index=False, sep='\t')

Loading