def runPy():
import hexagram
rootDir = '/Users/swat/hex-stats'
inDir = 'pyIn/'
class Options:
def __init__(s):
s.associations = True
s.colormaps = inDir + 'colormaps.txt'
s.directory = 'pyOutTest'
s.drlpath = None
s.html = 'test.dat'
s.mi_binary_binning = True
s.mi_window_size = 25
s.mi_window_threshold = 30
s.mutualinfo = True
s.names = ['mRNA seq']
s.query = None
s.raw = None
s.rawsim = None
s.scores = [inDir + 'old_attributes.csv']
s.similarity = [inDir + 'artificial_sparse.tab']
s.singletons = False
s.stats = True
s.truncation_edges = 10
s.type = None
s.window_size = 20
def printIt(s):
print json.dumps(s, indent=4, sort_keys=True)
options = Options();
os.chdir(rootDir)
hexagram.hexIt(options)
os.chdir('tests/unittest')
def hexIt(s):
global inDir, outDir
class Options:
global inDir, outDir
def __init__(s):
s.associations = True
s.colormaps = inDir + 'colormaps.txt'
s.directory = outDir
s.drlpath = None
s.html = 'test.dat'
s.mi_window_size = 25
s.mi_window_threshold = 4 # 30
s.mutualinfo = True
s.names = ['mRNA seq']
s.query = None
s.raw = None
s.rawsim = None
s.scores = [inDir + 'old_attributes.csv']
s.similarity = [inDir + 'artificial_sparse.tab']
s.singletons = False
s.stats = True
s.truncation_edges = 10
s.type = None
s.window_size = 25
def printIt(s):
print json.dumps(s, indent=4, sort_keys=True)
os.chdir(serverDir)
s.options = Options()
shutil.rmtree(outDir)
hexagram.hexIt(s.options)
def hexIt(s):
global inDir, outDir
class Options:
global inDir, outDir
def __init__(s):
s.associations = True
s.colormaps = inDir + 'colormaps.txt'
s.directory = outDir
s.drlpath = None
s.html = 'test.dat'
s.mi_window_size = 25
s.mi_window_threshold = 4 # 30
s.mutualinfo = True
s.names = ['mRNA seq']
s.query = None
s.raw = None
s.rawsim = None
s.scores = [inDir + 'old_attributes.csv']
s.similarity = [inDir + 'artificial_sparse.tab']
s.singletons = False
s.stats = True
s.truncation_edges = 10
s.type = None
s.window_size = 25
def printIt(s):
print json.dumps(s, indent=4, sort_keys=True)
os.chdir(serverDir)
s.options = Options();
shutil.rmtree(outDir)
hexagram.hexIt(s.options)
def runPy():
rootDir = '/Users/swat/dev/hexagram/'
serverDir = rootDir + 'server/'
inDir = rootDir + 'tests/pyUnittest/pyIn/'
outDir = rootDir + 'tests/pyUnittest/pyOutTest/'
testDir = rootDir + 'tests/pyUnittest'
print 'serverDir', serverDir
sys.path.append(serverDir)
import hexagram
"""
python /data/medbook-galaxy-central/tools/hexagram/hexagram.py \
"/data/signatures/TCGA/PANCAN/paper/sparse_matrices/spearman/mRNA_pancan12_self_SPEARMAN_top_50" \
"/data/signatures/TCGA/PANCAN/paper/sparse_matrices/spearman/cn_pancan12_self_SPEARMAN_top_50.tab" \
--names "mRNA Seq" \
--names "SCNA" \
--scores "/data/signatures/TCGA/PANCAN/paper/attributes/genomic_events,_breast_subtype_,_tissue_scores.tab" \
--scores "/data/signatures/TCGA/PANCAN/paper/subtypes/OV-Subtypes.tab" \
--colormaps "/data/signatures/TCGA/PANCAN/paper/subtypes/colormaps.tab" \
--html "/data/database/files/014/dataset_14909.dat" \
--directory "hex_temp" \
--truncation_edges 10
"""
class Options:
def __init__(s):
s.associations = True
s.colormaps = inDir + 'colormaps.txt'
s.directory = outDir
s.drlpath = None
s.html = 'test.dat'
s.mi_window_size = 25
s.mi_window_threshold = 4 # 30 default
s.mutualinfo = True
s.names = ['mRNA seq']
s.query = None
s.raw = None
s.rawsim = None
s.scores = [inDir + 'old_attributes.csv']
s.similarity = [inDir + 'artificial_sparse.tab']
s.singletons = False
s.stats = True
s.truncation_edges = 10
s.type = None
s.window_size = 20
def printIt(s):
print json.dumps(s, indent=4, sort_keys=True)
options = Options()
os.chdir(serverDir)
hexagram.hexIt(options)
os.chdir(rootDir + 'tests/pyUnittest')
def runPy():
rootDir = '/Users/swat/dev/hexagram/'
serverDir = rootDir + 'server/'
inDir = rootDir + 'tests/pyUnittest/pyIn/'
outDir = rootDir + 'tests/pyUnittest/pyOutTest/'
testDir = rootDir + 'tests/pyUnittest'
print 'serverDir', serverDir
sys.path.append(serverDir)
import hexagram
"""
python /data/medbook-galaxy-central/tools/hexagram/hexagram.py \
"/data/signatures/TCGA/PANCAN/paper/sparse_matrices/spearman/mRNA_pancan12_self_SPEARMAN_top_50" \
"/data/signatures/TCGA/PANCAN/paper/sparse_matrices/spearman/cn_pancan12_self_SPEARMAN_top_50.tab" \
--names "mRNA Seq" \
--names "SCNA" \
--scores "/data/signatures/TCGA/PANCAN/paper/attributes/genomic_events,_breast_subtype_,_tissue_scores.tab" \
--scores "/data/signatures/TCGA/PANCAN/paper/subtypes/OV-Subtypes.tab" \
--colormaps "/data/signatures/TCGA/PANCAN/paper/subtypes/colormaps.tab" \
--html "/data/database/files/014/dataset_14909.dat" \
--directory "hex_temp" \
--truncation_edges 10
"""
class Options:
def __init__(s):
s.associations = True
s.colormaps = inDir + 'colormaps.txt'
s.directory = outDir
s.drlpath = None
s.html = 'test.dat'
s.mi_window_size = 25
s.mi_window_threshold = 4 # 30 default
s.mutualinfo = True
s.names = ['mRNA seq']
s.query = None
s.raw = None
s.rawsim = None
s.scores = [inDir + 'old_attributes.csv']
s.similarity = [inDir + 'artificial_sparse.tab']
s.singletons = False
s.stats = True
s.truncation_edges = 10
s.type = None
s.window_size = 20
def printIt(s):
print json.dumps(s, indent=4, sort_keys=True)
options = Options();
os.chdir(serverDir)
hexagram.hexIt(options)
os.chdir(rootDir + 'tests/pyUnittest')