def read_tricol_bitscores(file_path,
net1=None,
net2=None,
by='name',
row_filter=None,
**kwargs):
if 'delimiter' not in kwargs:
kwargs['delimiter'] = '\t'
if row_filter is not None:
rows = [
row for row in iter_csv(file_path, **kwargs) if row_filter(row)
]
else:
rows = [row for row in iter_csv(file_path, **kwargs)]
return TricolBitscoreMatrix(rows, net1=net1, net2=net2, by=by)
def read_tsv_edgelist(*, path=None, string=None, header=False):
if string is not None:
return list(
iter_csv_fd(io.StringIO(string), delimiter='\t', header=header))
elif path is not None:
return list(iter_csv(path, delimiter='\t', header=header))
else:
return None
def import_alignment(self,
net1,
net2,
execution_dir,
file_name='alignment-net1-net2.tab'):
header = (net1.name, net2.name)
align_path = path.join(execution_dir, file_name)
return header, [(a.strip(), b.strip())
for a, b in iter_csv(align_path, delimiter='\t')]
def import_alignment(self,
net1,
net2,
execution_dir,
file_name='net1_net2.pinalog.nodes_algn.txt'):
header = (net1.name, net2.name)
align_path = path.join(execution_dir, file_name)
return header, [
(a, b) for a, b, some_score in iter_csv(align_path, delimiter='\t')
]
def iter_alignment_ids(self,
execution_dir,
file_name='alignment-net1-net2.csv'):
alignment_path = path.join(execution_dir, file_name)
# ignore the first two lines, they seem to be comments
csv_rows = iter_csv(alignment_path, delimiter=' ')
csv_rows = islice(csv_rows, 2, None)
for p1id, p2id in csv_rows:
yield int(p1id), int(p2id)
def import_alignment(self,
net1,
net2,
execution_dir,
file_name='net1.tab-net2.tab.alignment'):
align_path = path.join(execution_dir, file_name)
alignment = [(a, b) for a, b in iter_csv(
align_path, delimiter=' ', skipinitialspace=False)
if a != '' and b != '']
header = (net1.name, net2.name)
if net1.igraph.vcount() > net2.igraph.vcount():
alignment = [(b, a) for a, b in alignment]
return header, alignment