diff options
Diffstat (limited to 'wqflask/maintenance')
| -rw-r--r-- | wqflask/maintenance/convert_geno_to_bimbam.py | 6 | ||||
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 8 | ||||
| -rw-r--r-- | wqflask/maintenance/generate_kinship_from_bimbam.py | 4 | ||||
| -rw-r--r-- | wqflask/maintenance/geno_to_json.py | 4 | ||||
| -rw-r--r-- | wqflask/maintenance/quantile_normalize.py | 16 | ||||
| -rw-r--r-- | wqflask/maintenance/set_resource_defaults.py | 30 |
6 files changed, 34 insertions, 34 deletions
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py index c5af1ca6..078be529 100644 --- a/wqflask/maintenance/convert_geno_to_bimbam.py +++ b/wqflask/maintenance/convert_geno_to_bimbam.py @@ -56,7 +56,7 @@ class ConvertGenoFile: '@pat': "0", '@het': "0.5", '@unk': "NA" - } + } self.configurations = {} self.input_fh = open(self.input_file) @@ -171,7 +171,7 @@ class ConvertGenoFile: snp_output_file = os.path.join( new_directory, group_name + "_snps.txt") output_files = [geno_output_file, - pheno_output_file, snp_output_file] + pheno_output_file, snp_output_file] print("%s -> %s" % ( os.path.join(old_directory, input_file), geno_output_file)) convertob = ConvertGenoFile(input_file, output_files) @@ -184,7 +184,7 @@ class ConvertGenoFile: print(" Exception:", why) print(traceback.print_exc()) print(" Found in row %s at tabular column %s" % (convertob.latest_row_pos, - convertob.latest_col_pos)) + convertob.latest_col_pos)) print(" Column is:", convertob.latest_col_value) print(" Row is:", convertob.latest_row_value) break diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 484336a6..db65a11f 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -62,10 +62,10 @@ def parse_db_uri(): parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( - db=parsed_uri.path[1:], - host=parsed_uri.hostname, - user=parsed_uri.username, - passwd=parsed_uri.password) + db=parsed_uri.path[1:], + host=parsed_uri.hostname, + user=parsed_uri.username, + passwd=parsed_uri.password) print(db_conn_info) return db_conn_info diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py index cd39fceb..9f01d094 100644 --- a/wqflask/maintenance/generate_kinship_from_bimbam.py +++ b/wqflask/maintenance/generate_kinship_from_bimbam.py @@ -23,7 +23,7 @@ class GenerateKinshipMatrices: def generate_kinship(self): gemma_command = "/gnu/store/xhzgjr0jvakxv6h3blj8z496xjig69b0-profile/bin/gemma -g " + self.geno_file + \ " -p " + self.pheno_file + \ - " -gk 1 -outdir /home/zas1024/genotype_files/genotype/bimbam/ -o " + self.group_name + " -gk 1 -outdir /home/zas1024/genotype_files/genotype/bimbam/ -o " + self.group_name print("command:", gemma_command) os.system(gemma_command) @@ -52,7 +52,7 @@ class GenerateKinshipMatrices: print(" Exception:", why) print(traceback.print_exc()) print(" Found in row %s at tabular column %s" % (convertob.latest_row_pos, - convertob.latest_col_pos)) + convertob.latest_col_pos)) print(" Column is:", convertob.latest_col_value) print(" Row is:", convertob.latest_row_value) break diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py index c74489a8..32e0e34b 100644 --- a/wqflask/maintenance/geno_to_json.py +++ b/wqflask/maintenance/geno_to_json.py @@ -63,7 +63,7 @@ class ConvertGenoFile: '@pat': "0", '@het': "0.5", '@unk': "NA" - } + } self.configurations = {} #self.skipped_cols = 3 @@ -172,7 +172,7 @@ class ConvertGenoFile: print(" Exception:", why) print(traceback.print_exc()) print(" Found in row %s at tabular column %s" % (convertob.latest_row_pos, - convertob.latest_col_pos)) + convertob.latest_col_pos)) print(" Column is:", convertob.latest_col_value) print(" Row is:", convertob.latest_row_value) break diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py index ac7689f5..88bb2cb5 100644 --- a/wqflask/maintenance/quantile_normalize.py +++ b/wqflask/maintenance/quantile_normalize.py @@ -21,10 +21,10 @@ def parse_db_uri(): parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( - db=parsed_uri.path[1:], - host=parsed_uri.hostname, - user=parsed_uri.username, - passwd=parsed_uri.password) + db=parsed_uri.path[1:], + host=parsed_uri.hostname, + user=parsed_uri.username, + passwd=parsed_uri.password) print(db_conn_info) return db_conn_info @@ -70,10 +70,10 @@ def set_data(dataset_name): trait_name = line1.split('\t')[0] for i, sample in enumerate(sample_names): this_sample = { - "name": sample, - "value": line1.split('\t')[i + 1], - "qnorm": line2.split('\t')[i + 1] - } + "name": sample, + "value": line1.split('\t')[i + 1], + "qnorm": line2.split('\t')[i + 1] + } sample_list.append(this_sample) query = """SELECT Species.SpeciesName, InbredSet.InbredSetName, ProbeSetFreeze.FullName FROM Species, InbredSet, ProbeSetFreeze, ProbeFreeze, ProbeSetXRef, ProbeSet diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py index c6c4f44c..0f472494 100644 --- a/wqflask/maintenance/set_resource_defaults.py +++ b/wqflask/maintenance/set_resource_defaults.py @@ -44,10 +44,10 @@ def parse_db_uri(): parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( - db=parsed_uri.path[1:], - host=parsed_uri.hostname, - user=parsed_uri.username, - passwd=parsed_uri.password) + db=parsed_uri.path[1:], + host=parsed_uri.hostname, + user=parsed_uri.username, + passwd=parsed_uri.password) print(db_conn_info) return db_conn_info @@ -69,12 +69,12 @@ def insert_probeset_resources(default_owner_id): resource_ob['type'] = "dataset-probeset" if resource[2] < 1 and resource[3] > 0: resource_ob['default_mask'] = {"data": "view", - "metadata": "view", - "admin": "not-admin"} + "metadata": "view", + "admin": "not-admin"} else: resource_ob['default_mask'] = {"data": "no-access", - "metadata": "no-access", - "admin": "not-admin"} + "metadata": "no-access", + "admin": "not-admin"} resource_ob['group_masks'] = {} add_resource(resource_ob, update=False) @@ -101,11 +101,11 @@ def insert_publish_resources(default_owner_id): resource_ob['name'] = str(resource[0]) resource_ob['owner_id'] = default_owner_id resource_ob['data'] = {"dataset": str(resource[1]), - "trait": str(resource[0])} + "trait": str(resource[0])} resource_ob['type'] = "dataset-publish" resource_ob['default_mask'] = {"data": "view", - "metadata": "view", - "admin": "not-admin"} + "metadata": "view", + "admin": "not-admin"} resource_ob['group_masks'] = {} @@ -133,12 +133,12 @@ def insert_geno_resources(default_owner_id): resource_ob['type'] = "dataset-geno" if resource[2] < 1: resource_ob['default_mask'] = {"data": "view", - "metadata": "view", - "admin": "not-admin"} + "metadata": "view", + "admin": "not-admin"} else: resource_ob['default_mask'] = {"data": "no-access", - "metadata": "no-access", - "admin": "not-admin"} + "metadata": "no-access", + "admin": "not-admin"} resource_ob['group_masks'] = {} add_resource(resource_ob, update=False) |