def __init__(self, cmembers_file, alpha):
# Most attributes are unused
self.num_merges = 0
self.merge_order = []
self.pplinks_file = None
self.score_cutoff = None
self.cmembers_file = cmembers_file
self.alpha = alpha
self.beta = None
self.rtol = None
self.weight_range = itermerge.ITM_WEIGHTS_MEMBERS
self.min_pc_count = None
self.min_pp_count = None
self.shuffle = False
self.clusters = None
self.G = None
self.proteins = None
self.SPL = None
self.p2c_counts = None
self.adb = AssociationDatabase.load(cmembers_file)
self.pp_edges = None
self._initialize_clusters()
def complex(cmembers_file, output_file, complex_id):
adb = AssociationDatabase.load(cmembers_file)
if output_file == '-':
fp = sys.stdout
else:
fp = open(output_file, 'w')
cls = adb[complex_id]
cls.write_line2(fp)
def p2c(cmembers_file, output_file):
p2c_counts = defaultdict(int)
adb = AssociationDatabase.load(cmembers_file)
for evd in adb.associations():
for p in evd.proteins:
if evd.proteins[p][1] > 0.0:
p2c_counts[p] += 1
items = sorted(p2c_counts.iteritems(), key=itemgetter(1, 0))
with open(output_file, 'w') as fp:
for i, row in enumerate(items):
fp.write('{}\t{}\t{}\n'.format(i, *row))
def __init__(self,
pplinks_file,
cmembers_file,
alpha,
beta,
rtol,
score_cutoff=0.21,
weight_range=ITM_WEIGHTS_MEMBERS,
initial_merge_order=None,
min_pc_count=1,
min_pp_count=1,
shuffle=False):
self.num_merges = 0
self.merge_order = []
self.pplinks_file = pplinks_file
self.score_cutoff = score_cutoff
self.cmembers_file = cmembers_file
self.alpha = alpha
self.beta = beta
self.rtol = AssocCluster.rtol = rtol
self.weight_range = AssocCluster.weight_range = weight_range
self.min_pc_count = min_pc_count
self.min_pp_count = min_pp_count
self.shuffle = shuffle
self.clusters = None
self.G = None
self.proteins = None
self.SPL = None
self.p2c_counts = None
self.adb = AssociationDatabase.load(cmembers_file)
self.pp_edges = infflow.load_pp_edges(self.pplinks_file,
self.score_cutoff)
self._set_minimum_counts()
if self.beta >= 1.0:
self._find_beta()
self._get_pp_solver()
self._initialize_clusters(initial_merge_order)
def pubmed(cmembers_file, stats_file):
adb = AssociationDatabase.load(cmembers_file)
with open(stats_file, 'w') as fp:
adb.write_pubmed_stats(fp)
def details(cmembers_file, output_file):
adb = AssociationDatabase.load(cmembers_file)
with open(output_file, 'w') as fp:
adb.write_details(fp)