diff options
| -rw-r--r-- | gn3/db/datasets.py | 30 |
1 files changed, 15 insertions, 15 deletions
diff --git a/gn3/db/datasets.py b/gn3/db/datasets.py index 48cd195..470e430 100644 --- a/gn3/db/datasets.py +++ b/gn3/db/datasets.py @@ -12,25 +12,25 @@ def retrieve_sample_list(group: str): the "official" sample list is stored """ + samplelist = [] genofile_path = os.environ.get("GENENETWORK_FILES") + "/genotype/" + group + ".geno" if os.path.isfile(genofile_path): - genofile = open(genofile_path) + with open(genofile_path, "r") as genofile: + for line in genofile: + line = line.strip() + if not line: + continue + if line.startswith(("#", "@")): + continue + break - for line in genofile: - line = line.strip() - if not line: - continue - if line.startswith(("#", "@")): - continue - break + headers = line.split("\t") - headers = line.split("\t") - - if headers[3] == "Mb": - samplelist = headers[4:] - else: - samplelist = headers[3:] - return samplelist + if headers[3] == "Mb": + samplelist = headers[4:] + else: + samplelist = headers[3:] + return samplelist def retrieve_group_name( group_id: int, connection: any): |