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feat([st]rwr): consider weights #441

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feat([st]rwr): consider weights #441

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6 changes: 3 additions & 3 deletions spras/rwr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ def generate_inputs(data, filename_map):
edges = data.get_interactome()
edges = convert_undirected_to_directed(edges)

edges.to_csv(filename_map['network'],sep='|',index=False,columns=['Interactor1','Interactor2'],header=False)
edges.to_csv(filename_map['network'],sep='|',index=False,columns=['Interactor1', 'Interactor2', 'Weight'],header=False)

@staticmethod
def run(network=None, nodes=None, alpha=None, output_file=None, container_settings=None, threshold=None):
Expand All @@ -47,8 +47,8 @@ def run(network=None, nodes=None, alpha=None, output_file=None, container_settin
for line in network_f:
line = line.strip()
endpoints = line.split("|")
if len(endpoints) != 2:
raise ValueError(f"Edge {line} does not contain 2 nodes separated by '|'")
if len(endpoints) != 3:
raise ValueError(f"Edge {line} does not contain 2 nodes and 1 weight separated by '|'")
work_dir = '/spras'

# Each volume is a tuple (src, dest)
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6 changes: 3 additions & 3 deletions spras/strwr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ def generate_inputs(data, filename_map):
edges = data.get_interactome()
edges = convert_undirected_to_directed(edges)

edges.to_csv(filename_map['network'],sep='|',index=False,columns=['Interactor1','Interactor2'],header=False)
edges.to_csv(filename_map['network'],sep='|',index=False,columns=['Interactor1', 'Interactor2', 'Weight'],header=False)

@staticmethod
def run(network=None, sources=None, targets=None, alpha=None, output_file=None, container_settings=None, threshold=None):
Expand All @@ -47,8 +47,8 @@ def run(network=None, sources=None, targets=None, alpha=None, output_file=None,
for line in network_f:
line = line.strip()
endpoints = line.split("|")
if len(endpoints) != 2:
raise ValueError(f"Edge {line} does not contain 2 nodes separated by '|'")
if len(endpoints) != 3:
raise ValueError(f"Edge {line} does not contain 2 nodes and 1 weight separated by '|'")

work_dir = '/spras'

Expand Down
10 changes: 5 additions & 5 deletions test/RWR/input/rwr-bad-network.txt
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
A|B|F
A|C
B|D
C|B
C|E
A|B|1|F
A|C|1
B|D|1
C|B|1
C|E|1
10 changes: 5 additions & 5 deletions test/RWR/input/rwr-network.txt
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
A|B
A|C
B|D
C|B
C|E
A|B|1
A|C|1
B|D|1
C|B|1
C|E|1
10 changes: 5 additions & 5 deletions test/ST_RWR/input/strwr-bad-network.txt
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
A|B|F
A|C
B|D
C|B
C|E
A|B|1|F
A|C|1
B|D|1
C|B|1
C|E|1
10 changes: 5 additions & 5 deletions test/ST_RWR/input/strwr-network.txt
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
A|B
A|C
B|D
C|B
C|E
A|B|1
A|C|1
B|D|1
C|B|1
C|E|1
8 changes: 4 additions & 4 deletions test/generate-inputs/expected/rwr-network-expected.txt
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
test_A|B
B|C
B|test_A
C|B
test_A|B|0.98
B|C|0.77
B|test_A|0.98
C|B|0.77
8 changes: 4 additions & 4 deletions test/generate-inputs/expected/strwr-network-expected.txt
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Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
test_A|B
B|C
B|test_A
C|B
test_A|B|0.98
B|C|0.77
B|test_A|0.98
C|B|0.77
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