def _translate_gene_list(gene_list):
"""gene_list can already be a sequence of strings or it could be a path to
a file that contains a list of strings.
The path can be relative to the data directory or an absolute path.
The file can be any format supported by read_strings_from_file()
"""
# if it's not something that could be a filename assume it's a sequence of strings
if not isinstance(gene_list, basestring):
return None, gene_list
# try to find a matching filename and read the data from it
pathway_name = splitext(basename(gene_list))[
0] # use the file's basename (without extension) as the pathway name
for path in [
gene_list,
join(project_dirs.data_dir(), gene_list),
join(project_dirs.pathways_dir(), gene_list)
]:
if isfile(path):
if cfg.verbosity > 0:
print 'Reading gene list from {}'.format(path)
gene_list = read_strings_from_file(path)
return pathway_name, gene_list
# not found
return None, None
def list_to_pathway_names(listname):
if listname == 'all':
pathway_names = [f[:-4] for f in listdir(pathways_dir()) if f.endswith('.txt')]
else:
listfile = join(pathway_lists_dir(),listname)
with open(listfile) as f:
lines = f.readlines()
pathway_names = [x.strip() for x in lines] # remove newlines
pathway_names = [x for x in pathway_names if x] # rmeove empty strings
return pathway_names
def _translate_gene_list(gene_list):
"""gene_list can already be a sequence of strings or it could be a path to
a file that contains a list of strings.
The path can be relative to the data directory or an absolute path.
The file can be any format supported by read_strings_from_file()
"""
# if it's not something that could be a filename assume it's a sequence of strings
if not isinstance(gene_list, basestring):
return None, gene_list
# try to find a matching filename and read the data from it
pathway_name = splitext(basename(gene_list))[0] # use the file's basename (without extension) as the pathway name
for path in [gene_list, join(project_dirs.data_dir(),gene_list), join(project_dirs.pathways_dir(),gene_list)]:
if isfile(path):
if cfg.verbosity > 0:
print 'Reading gene list from {}'.format(path)
gene_list = read_strings_from_file(path)
return pathway_name, gene_list
# not found
return None,None
def read_pathway(pathway):
filename = join(pathways_dir(), pathway + '.txt')
with open(filename) as f:
lines = f.readlines()
genes = [x.strip() for x in lines] # remove newlines
return [x for x in genes if x] # rmeove empty strings
