releasing version v1.0

sfu-compbio · Mar 27, 2020 · 45cd0c7 · 45cd0c7
1 parent ff377e4
commit 45cd0c7
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Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/PhISCS-B/__main__.py b/PhISCS-B/__main__.py
@@ -64,17 +64,18 @@
 
 filename = os.path.splitext(os.path.basename(args.SCFile))[0]
 outfile = os.path.join(args.outDir, filename)
+dirname = os.path.dirname(__file__)
 
 if args.solver.lower() == 'z3':
     if usingBulk:
-        cmds = ['python', 'PhISCS-B/csp_z3.py', '-f', args.SCFile, '-n', args.fnProbability, '-p', args.fpProbability, 
+        cmds = ['python', '{}/csp_z3.py'.format(dirname), '-f', args.SCFile, '-n', args.fnProbability, '-p', args.fpProbability, 
                 '-w', args.colEliminationWeight, '-o', args.outDir, '-t 1', '--timeout', args.time, '-e', args.delta,
                 '-b', args.bulkFile, '-m', args.maxMutationsToEliminate]
     else:
-        cmds = ['python', 'PhISCS-B/csp_z3.py', '-f', args.SCFile, '-n', args.fnProbability, '-p', args.fpProbability, 
+        cmds = ['python', '{}/csp_z3.py'.format(dirname), '-f', args.SCFile, '-n', args.fnProbability, '-p', args.fpProbability, 
                 '-w', args.colEliminationWeight, '-o', args.outDir, '-t 1', '--timeout', args.time, '-m', args.maxMutationsToEliminate]
 else:
-    cmds = ['PhISCS-B/csp_maxsat', '-f', args.SCFile, '-n', args.fnProbability, '-p', args.fpProbability, '-o', args.outDir, '-i']
+    cmds = ['{}/csp_maxsat'.format(dirname), '-f', args.SCFile, '-n', args.fnProbability, '-p', args.fpProbability, '-o', args.outDir, '-i']
 
 cmd = ' '.join(str(v) for v in cmds)
 # print(cmd)

diff --git a/PhISCS-B/helperFunctions.py b/PhISCS-B/helperFunctions.py
@@ -62,7 +62,7 @@ def draw_tree(filename, addBulk, bulkfile):
     import pandas as pd
     import pygraphviz as pyg
 
-    graph = pyg.AGraph(strict=False, directed=True)
+    graph = pyg.AGraph(strict=False, directed=True, dpi=300)
     font_name = 'Avenir'
 
     class Node:

diff --git a/PhISCS-I/helperFunctions.py b/PhISCS-I/helperFunctions.py
@@ -469,7 +469,7 @@ def write_tree(matrix, names):
 
 
 def draw_farid(filename, addBulk, bulkfile):
-    add_cells=False
+    add_cells=True
 
     import pandas as pd
     import pygraphviz as pyg