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Update MCF Wrapper Code #144

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Update MCF Wrapper Code #144

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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
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4 changes: 2 additions & 2 deletions .github/workflows/test-spras.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,7 @@ jobs:
docker pull reedcompbio/omics-integrator-2:v2
docker pull reedcompbio/pathlinker:v2
docker pull reedcompbio/meo:latest
docker pull reedcompbio/mincostflow:latest
docker pull reedcompbio/mincostflow:v2
docker pull reedcompbio/allpairs:v2
docker pull reedcompbio/domino:latest
docker pull reedcompbio/py4cytoscape:v2
Expand Down Expand Up @@ -126,7 +126,7 @@ jobs:
path: docker-wrappers/MinCostFlow/.
dockerfile: docker-wrappers/MinCostFlow/Dockerfile
repository: reedcompbio/mincostflow
tags: latest
tags: v2
cache_froms: reedcompbio/mincostflow:latest
push: false
- name: Build All Pairs Shortest Paths Docker image
Expand Down
4 changes: 4 additions & 0 deletions docker-wrappers/MinCostFlow/README.md
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Expand Up @@ -36,3 +36,7 @@ docker run -w /data --mount type=bind,source=/${PWD},target=/data reedcompbio/mi
This will run MinCostFlow on the test input files and write the output files to the root of the `spras` repository.

Windows users may need to escape the absolute paths so that `/data` becomes `//data`, etc.

## Versions
- v1: Initial version. Handles undirected edges only.
- v2: Updated to handle both directed and undirected edges.
12 changes: 3 additions & 9 deletions spras/mincostflow.py
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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 @@ -114,7 +111,7 @@ def run(sources=None, targets=None, edges=None, output_file=None, flow=None, cap
command.extend(['--capacity', str(capacity)])

# choosing to run in docker or singularity container
container_suffix = "mincostflow"
container_suffix = "mincostflow:v2"

# constructs a docker run call
out = run_container(container_framework,
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')

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