diff options
54 files changed, 509 insertions, 509 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 5eac695e..e20f2f98 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -151,7 +151,7 @@ class DatasetType: "WHERE InbredSet.Name = '%s' AND " "PublishFreeze.InbredSetId = InbredSet.Id"), 'geno': ("SELECT GenoFreeze.Id FROM GenoFreeze WHERE " - "GenoFreeze.Name = \"%s\" ") + "GenoFreeze.Name = \"%s\" ") } dataset_name_mapping = { 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) diff --git a/wqflask/tests/unit/base/test_webqtl_case_data.py b/wqflask/tests/unit/base/test_webqtl_case_data.py index cebd41ce..e1555cb4 100644 --- a/wqflask/tests/unit/base/test_webqtl_case_data.py +++ b/wqflask/tests/unit/base/test_webqtl_case_data.py @@ -10,10 +10,10 @@ class TestWebqtlCaseData(unittest.TestCase): def setUp(self): self.w = webqtlCaseData(name="Test", - value=0, - variance=0.0, - num_cases=10, - name2="Test2") + value=0, + variance=0.0, + num_cases=10, + name2="Test2") def test_webqtl_case_data_repr(self): self.assertEqual( diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py index 34ffa9ef..1089a36f 100644 --- a/wqflask/tests/unit/wqflask/api/test_correlation.py +++ b/wqflask/tests/unit/wqflask/api/test_correlation.py @@ -106,9 +106,9 @@ class TestCorrelations(unittest.TestCase): target_vals = [3.4, 6.2, 4.1, 3.4, 1.2, 5.6] trait_data = {"S1": AttributeSetter({"value": 2.3}), "S2": AttributeSetter({"value": 1.1}), - "S3": AttributeSetter( + "S3": AttributeSetter( {"value": 6.3}), "S4": AttributeSetter({"value": 3.6}), "S5": AttributeSetter({"value": 4.1}), - "S6": AttributeSetter({"value": 5.0})} + "S6": AttributeSetter({"value": 5.0})} this_trait = AttributeSetter({"data": trait_data}) mock_normalize.return_value = ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0], [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py index 5cbaf0e0..4003d68f 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py @@ -162,13 +162,13 @@ X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6""" results = parse_loco_output( this_dataset={}, gwa_output_filename=".xw/") expected_results = [ - {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85, - 'additive': 23.3, 'lod_score': 0.07058107428570727}, - {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, - 'additive': 24.0, 'lod_score': 0.3010299956639812}, - {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, - 'additive': 11.6, 'lod_score': 0.1549019599857432}, - {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': 21.1, 'lod_score': 0.22184874961635637}] + {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85, + 'additive': 23.3, 'lod_score': 0.07058107428570727}, + {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, + 'additive': 24.0, 'lod_score': 0.3010299956639812}, + {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, + 'additive': 11.6, 'lod_score': 0.1549019599857432}, + {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': 21.1, 'lod_score': 0.22184874961635637}] self.assertEqual(expected_results, results) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py index 47377873..93848a84 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py @@ -18,6 +18,6 @@ class TestQtlReaperMapping(unittest.TestCase): mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt", "w") filehandler = mock_open() write_calls = [mock.call('Trait\t'), mock.call( - 'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')] + 'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')] filehandler.write.assert_has_calls(write_calls) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py index e518ec22..68686e27 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py @@ -21,7 +21,7 @@ class TestRqtlMapping(unittest.TestCase): """test for getting trait data_type return True""" query_value = """SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" mock_db.db.execute.return_value.fetchone.return_value = [ - """{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] + """{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] results = get_trait_data_type("traid_id") mock_db.db.execute.assert_called_with(query_value) self.assertEqual(results, "fer434f") diff --git a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py index 8823e1fc..89442c47 100644 --- a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py +++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py @@ -22,10 +22,10 @@ class TestSnpBrowser(unittest.TestCase): strains = {"mouse": ["S1", "S2", "S3", "S4", "S5"], "rat": []} expected_results = ([['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'ConScore', 'Domain 1', 'Domain 2', 'Details'], - ['S1', 'S2', 'S3', 'S4', 'S5']], 5, - ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles', - 'conservation_score', 'domain_1', 'domain_2', - 'function_details', 'S1', 'S2', 'S3', 'S4', 'S5']) + ['S1', 'S2', 'S3', 'S4', 'S5']], 5, + ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles', + 'conservation_score', 'domain_1', 'domain_2', + 'function_details', 'S1', 'S2', 'S3', 'S4', 'S5']) results_with_snp = get_header_list( variant_type="SNP", strains=strains, species="Mouse", empty_columns=empty_columns) @@ -34,8 +34,8 @@ class TestSnpBrowser(unittest.TestCase): expected_results_with_indel = ( ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'], 0, - ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s', - 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name']) + ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s', + 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name']) self.assertEqual(expected_results, results_with_snp) self.assertEqual(expected_results_with_indel, results_with_indel) diff --git a/wqflask/tests/unit/wqflask/test_server_side.py b/wqflask/tests/unit/wqflask/test_server_side.py index 9d988aea..be7ca2df 100644 --- a/wqflask/tests/unit/wqflask/test_server_side.py +++ b/wqflask/tests/unit/wqflask/test_server_side.py @@ -23,7 +23,7 @@ class TestServerSideTableTests(unittest.TestCase): ] headers = ['first', 'second', 'third'] request_args = {'sEcho': '1', 'iSortCol_0': '1', 'iSortingCols': '1', - 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'} + 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'} test_page = ServerSideTable( rows_count, table_rows, headers, request_args).get_page() diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index f61e3b88..37a8a1a5 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -206,7 +206,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab im_drawer.text( text=strY, xy=(xLeftOffset - im_drawer.textsize(strY, - font=scaleFont)[0] - 6, yc + 5), + font=scaleFont)[0] - 6, yc + 5), font=scaleFont) y += (yTop - yLow) / stepY diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py index 6c8cd546..25273fa0 100644 --- a/wqflask/utility/__init__.py +++ b/wqflask/utility/__init__.py @@ -32,4 +32,4 @@ class Struct: def __repr__(self): return '{%s}' % str(', '.join('%s : %s' % (k, repr(v)) for - (k, v) in list(self.__dict__.items()))) + (k, v) in list(self.__dict__.items()))) diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py index 55907dd5..e56c22eb 100644 --- a/wqflask/utility/elasticsearch_tools.py +++ b/wqflask/utility/elasticsearch_tools.py @@ -50,7 +50,7 @@ from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT def test_elasticsearch_connection(): es = Elasticsearch(['http://' + ELASTICSEARCH_HOST + \ - ":" + str(ELASTICSEARCH_PORT) + '/'], verify_certs=True) + ":" + str(ELASTICSEARCH_PORT) + '/'], verify_certs=True) if not es.ping(): logger.warning("Elasticsearch is DOWN") diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py index eb545478..86d9823e 100644 --- a/wqflask/utility/genofile_parser.py +++ b/wqflask/utility/genofile_parser.py @@ -37,10 +37,10 @@ class ConvertGenoFile: self.input_fh = open(input_file) print("!!!!!!!!!!!!!!!!PARSER!!!!!!!!!!!!!!!!!!") self.haplotype_notation = { - '@mat': "1", - '@pat': "2", - '@het': "-999", - '@unk': "-999" + '@mat': "1", + '@pat': "2", + '@het': "-999", + '@unk': "-999" } self.configurations = {} @@ -93,7 +93,7 @@ class ConvertGenoFile: for item_count, genotype in enumerate(genotypes): if genotype.upper().strip() in self.configurations: this_marker.genotypes.append( - self.configurations[genotype.upper().strip()]) + self.configurations[genotype.upper().strip()]) else: print("WARNING:", genotype.upper()) this_marker.genotypes.append("NA") diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py index 05f8a2b0..6ef759e0 100644 --- a/wqflask/utility/startup_config.py +++ b/wqflask/utility/startup_config.py @@ -39,4 +39,4 @@ def app_config(): # es.test_elasticsearch_connection() print(("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % - (BLUE, str(port), ENDC, get_setting("WEBSERVER_URL")))) + (BLUE, str(port), ENDC, get_setting("WEBSERVER_URL")))) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 4f09176a..e28abb48 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -295,8 +295,8 @@ ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET') ORCID_AUTH_URL = None if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET: ORCID_AUTH_URL = "https://orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id=" + \ - ORCID_CLIENT_ID + "&client_secret=" + ORCID_CLIENT_SECRET + \ - "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2" + ORCID_CLIENT_ID + "&client_secret=" + ORCID_CLIENT_SECRET + \ + "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2" ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL') ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST') diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py index f355a865..0cb71567 100644 --- a/wqflask/utility/webqtlUtil.py +++ b/wqflask/utility/webqtlUtil.py @@ -35,29 +35,29 @@ from base import webqtlConfig # NL, 07/27/2010. moved from webqtlForm.py # Dict of Parents and F1 information, In the order of [F1, Mat, Pat] ParInfo = { -'BXH': ['BHF1', 'HBF1', 'C57BL/6J', 'C3H/HeJ'], -'AKXD': ['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'], -'BXD': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], -'C57BL-6JxC57BL-6NJF2': ['', '', 'C57BL/6J', 'C57BL/6NJ'], -'BXD300': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], -'B6BTBRF2': ['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'], -'BHHBF2': ['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'], -'BHF2': ['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'], -'B6D2F2': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], -'BDF2-1999': ['B6D2F2', 'D2B6F2', 'C57BL/6J', 'DBA/2J'], -'BDF2-2005': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], -'CTB6F2': ['CTB6F2', 'B6CTF2', 'C57BL/6J', 'Castaneous'], -'CXB': ['CBF1', 'BCF1', 'C57BL/6ByJ', 'BALB/cByJ'], -'AXBXA': ['ABF1', 'BAF1', 'C57BL/6J', 'A/J'], -'AXB': ['ABF1', 'BAF1', 'C57BL/6J', 'A/J'], -'BXA': ['BAF1', 'ABF1', 'C57BL/6J', 'A/J'], -'LXS': ['LSF1', 'SLF1', 'ISS', 'ILS'], -'HXBBXH': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'], -'BayXSha': ['BayXShaF1', 'ShaXBayF1', 'Bay-0', 'Shahdara'], -'ColXBur': ['ColXBurF1', 'BurXColF1', 'Col-0', 'Bur-0'], -'ColXCvi': ['ColXCviF1', 'CviXColF1', 'Col-0', 'Cvi'], -'SXM': ['SMF1', 'MSF1', 'Steptoe', 'Morex'], -'HRDP': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'] + 'BXH': ['BHF1', 'HBF1', 'C57BL/6J', 'C3H/HeJ'], + 'AKXD': ['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'], + 'BXD': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], + 'C57BL-6JxC57BL-6NJF2': ['', '', 'C57BL/6J', 'C57BL/6NJ'], + 'BXD300': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], + 'B6BTBRF2': ['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'], + 'BHHBF2': ['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'], + 'BHF2': ['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'], + 'B6D2F2': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], + 'BDF2-1999': ['B6D2F2', 'D2B6F2', 'C57BL/6J', 'DBA/2J'], + 'BDF2-2005': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'], + 'CTB6F2': ['CTB6F2', 'B6CTF2', 'C57BL/6J', 'Castaneous'], + 'CXB': ['CBF1', 'BCF1', 'C57BL/6ByJ', 'BALB/cByJ'], + 'AXBXA': ['ABF1', 'BAF1', 'C57BL/6J', 'A/J'], + 'AXB': ['ABF1', 'BAF1', 'C57BL/6J', 'A/J'], + 'BXA': ['BAF1', 'ABF1', 'C57BL/6J', 'A/J'], + 'LXS': ['LSF1', 'SLF1', 'ISS', 'ILS'], + 'HXBBXH': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'], + 'BayXSha': ['BayXShaF1', 'ShaXBayF1', 'Bay-0', 'Shahdara'], + 'ColXBur': ['ColXBurF1', 'BurXColF1', 'Col-0', 'Bur-0'], + 'ColXCvi': ['ColXCviF1', 'CviXColF1', 'Col-0', 'Cvi'], + 'SXM': ['SMF1', 'MSF1', 'Steptoe', 'Morex'], + 'HRDP': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'] } ######################################### diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py index 52026a82..870f3275 100644 --- a/wqflask/wqflask/api/correlation.py +++ b/wqflask/wqflask/api/correlation.py @@ -88,7 +88,7 @@ def calculate_results(this_trait, this_dataset, target_dataset, corr_params): corr_results = do_literature_correlation_for_all_traits( this_trait, this_dataset, trait_geneid_dict, corr_params) sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), - key=lambda t: -abs(t[1][1]))) + key=lambda t: -abs(t[1][1]))) else: for target_trait, target_vals in list(target_dataset.trait_data.items()): result = get_sample_r_and_p_values( diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py index e4a3fb77..cbef96eb 100644 --- a/wqflask/wqflask/api/mapping.py +++ b/wqflask/wqflask/api/mapping.py @@ -53,15 +53,15 @@ def do_mapping_for_api(start_vars): header_row = ["name", "chr", "cM", "lod_score"] if mapping_params['num_perm'] > 0: _sperm_output, _suggestive, _significant, result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'], - mapping_params['perm_check'], mapping_params['num_perm'], - mapping_params['do_control'], mapping_params[ - 'control_marker'], - mapping_params['manhattan_plot'], mapping_params['pair_scan']) + mapping_params['perm_check'], mapping_params['num_perm'], + mapping_params['do_control'], mapping_params[ + 'control_marker'], + mapping_params['manhattan_plot'], mapping_params['pair_scan']) else: result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'], - mapping_params['perm_check'], mapping_params['num_perm'], - mapping_params['do_control'], mapping_params['control_marker'], - mapping_params['manhattan_plot'], mapping_params['pair_scan']) + mapping_params['perm_check'], mapping_params['num_perm'], + mapping_params['do_control'], mapping_params['control_marker'], + mapping_params['manhattan_plot'], mapping_params['pair_scan']) if mapping_params['limit_to']: result_markers = result_markers[:mapping_params['limit_to']] diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index f7d52ca3..9d3446db 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -41,10 +41,10 @@ def get_species_list(): species_list = [] for species in the_species: species_dict = { - "Id": species[0], - "Name": species[1], - "FullName": species[2], - "TaxonomyId": species[3] + "Id": species[0], + "Name": species[1], + "FullName": species[2], + "TaxonomyId": species[3] } species_list.append(species_dict) @@ -60,10 +60,10 @@ def get_species_info(species_name, file_format="json"): the_species = results.fetchone() species_dict = { - "Id": the_species[0], - "Name": the_species[1], - "FullName": the_species[2], - "TaxonomyId": the_species[3] + "Id": the_species[0], + "Name": the_species[1], + "FullName": the_species[2], + "TaxonomyId": the_species[3] } return flask.jsonify(species_dict) @@ -92,12 +92,12 @@ def get_groups_list(species_name=None): groups_list = [] for group in the_groups: group_dict = { - "Id": group[0], - "SpeciesId": group[1], - "DisplayName": group[2], - "Name": group[3], - "FullName": group[4], - "public": group[5], + "Id": group[0], + "SpeciesId": group[1], + "DisplayName": group[2], + "Name": group[3], + "FullName": group[4], + "public": group[5], "MappingMethodId": group[6], "GeneticType": group[7] } @@ -137,12 +137,12 @@ def get_group_info(group_name, species_name=None, file_format="json"): group = results.fetchone() if group: group_dict = { - "Id": group[0], - "SpeciesId": group[1], - "DisplayName": group[2], - "Name": group[3], - "FullName": group[4], - "public": group[5], + "Id": group[0], + "SpeciesId": group[1], + "DisplayName": group[2], + "Name": group[3], + "FullName": group[4], + "public": group[5], "MappingMethodId": group[6], "GeneticType": group[7] } @@ -186,12 +186,12 @@ def get_datasets_for_group(group_name, species_name=None): datasets_list = [] for dataset in the_datasets: dataset_dict = { - "Id": dataset[0], - "ProbeFreezeId": dataset[1], - "AvgID": dataset[2], - "Short_Abbreviation": dataset[3], - "Long_Abbreviation": dataset[4], - "FullName": dataset[5], + "Id": dataset[0], + "ProbeFreezeId": dataset[1], + "AvgID": dataset[2], + "Short_Abbreviation": dataset[3], + "Long_Abbreviation": dataset[4], + "FullName": dataset[5], "ShortName": dataset[6], "CreateTime": dataset[7], "public": dataset[8], @@ -243,12 +243,12 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"): if dataset: dataset_dict = { - "dataset_type": "mRNA expression", - "id": dataset[0], - "name": dataset[1], - "full_name": dataset[2], - "short_name": dataset[3], - "data_scale": dataset[4], + "dataset_type": "mRNA expression", + "id": dataset[0], + "name": dataset[1], + "full_name": dataset[2], + "short_name": dataset[3], + "data_scale": dataset[4], "tissue_id": dataset[5], "tissue": dataset[6], "public": dataset[7], @@ -280,25 +280,25 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"): if dataset: if dataset[5]: dataset_dict = { - "dataset_type": "phenotype", - "id": dataset[0], - "name": dataset[1], - "description": dataset[2], - "pubmed_id": dataset[5], - "title": dataset[6], + "dataset_type": "phenotype", + "id": dataset[0], + "name": dataset[1], + "description": dataset[2], + "pubmed_id": dataset[5], + "title": dataset[6], "year": dataset[7] } elif dataset[4]: dataset_dict = { - "dataset_type": "phenotype", - "id": dataset[0], - "name": dataset[3], - "description": dataset[4] + "dataset_type": "phenotype", + "id": dataset[0], + "name": dataset[3], + "description": dataset[4] } else: dataset_dict = { - "dataset_type": "phenotype", - "id": dataset[0] + "dataset_type": "phenotype", + "id": dataset[0] } datasets_list.append(dataset_dict) @@ -364,7 +364,7 @@ def fetch_traits(dataset_name, file_format="json"): """ field_list = ["Id", "Name", "Symbol", "Description", "Chr", "Mb", - "Aliases", "Mean", "SE", "Locus", "LRS", "P-Value", "Additive", "h2"] + "Aliases", "Mean", "SE", "Locus", "LRS", "P-Value", "Additive", "h2"] elif data_type == "Geno": query = """ SELECT @@ -382,7 +382,7 @@ def fetch_traits(dataset_name, file_format="json"): """ field_list = ["Id", "Name", "Marker_Name", - "Chr", "Mb", "Sequence", "Source"] + "Chr", "Mb", "Sequence", "Source"] else: query = """ SELECT @@ -399,7 +399,7 @@ def fetch_traits(dataset_name, file_format="json"): """ field_list = ["Id", "PhenotypeId", "PublicationId", - "Locus", "LRS", "Additive", "Sequence"] + "Locus", "LRS", "Additive", "Sequence"] if 'limit_to' in request.args: limit_number = request.args['limit_to'] @@ -579,10 +579,10 @@ def trait_sample_data(dataset_name, trait_name, file_format="json"): sample_list = [] for sample in sample_data: sample_dict = { - "sample_name": sample[0], - "sample_name_2": sample[1], - "value": sample[2], - "data_id": sample[3], + "sample_name": sample[0], + "sample_name_2": sample[1], + "value": sample[2], + "data_id": sample[3], } if sample[4]: sample_dict["se"] = sample[4] @@ -626,10 +626,10 @@ def trait_sample_data(dataset_name, trait_name, file_format="json"): sample_list = [] for sample in sample_data: sample_dict = { - "sample_name": sample[0], - "sample_name_2": sample[1], - "value": sample[2], - "data_id": sample[3] + "sample_name": sample[0], + "sample_name_2": sample[1], + "value": sample[2], + "data_id": sample[3] } if sample[4]: sample_dict["se"] = sample[4] @@ -796,9 +796,9 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None): config_file = [filename + ".json", json.dumps(yaml_file)] #config_file = [filename + ".yaml", open("{0}/{1}.yaml".format(flat_files("genotype/rqtl2"), group_name))] geno_file = [filename + "_geno.csv", - open("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name))] + open("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name))] gmap_file = [filename + "_gmap.csv", - open("{0}/{1}_gmap.csv".format(flat_files("genotype/rqtl2"), group_name))] + open("{0}/{1}_gmap.csv".format(flat_files("genotype/rqtl2"), group_name))] if dataset_name: phenotypes = requests.get( "http://gn2.genenetwork.org/api/v_pre1/sample_data/" + dataset_name) @@ -828,7 +828,7 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None): if limit_num and i >= limit_num: break output_lines.append([line.strip() - for line in line.split(",")]) + for line in line.split(",")]) i += 1 csv_writer = csv.writer(si, delimiter=",") @@ -914,7 +914,7 @@ def get_dataset_trait_ids(dataset_name, start_vars): trait_ids = [result[0] for result in results] trait_names = [str(result[2]) + "_" + str(result[1]) - for result in results] + for result in results] return trait_ids, trait_names, data_type, dataset_id diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index b06d84ff..58518639 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -75,14 +75,14 @@ def collections_add(): if 'traits' in request.args: traits = request.args['traits'] return render_template("collections/add.html", - traits=traits, - collections=collections, + traits=traits, + collections=collections, ) else: hash = request.args['hash'] return render_template("collections/add.html", - hash=hash, - collections=collections, + hash=hash, + collections=collections, ) @@ -145,8 +145,8 @@ def list_collections(): user_collections = list(g.user_session.user_collections) return render_template("collections/list.html", - params=params, - collections=user_collections, + params=params, + collections=user_collections, ) @@ -225,7 +225,7 @@ def view_collection(): return json.dumps(json_version) else: return render_template("collections/view.html", - **collection_info + **collection_info ) diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py index d86c8e16..cb88eb53 100644 --- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py +++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py @@ -35,7 +35,7 @@ class ComparisonBarChart: def __init__(self, start_vars): trait_db_list = [trait.strip() - for trait in start_vars['trait_list'].split(',')] + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) @@ -90,8 +90,8 @@ class ComparisonBarChart: #print("dataset_name:", dataset_name) dataset_ob = data_set.create_dataset(dataset_name) trait_ob = create_trait(dataset=dataset_ob, - name=trait_name, - cellid=None) + name=trait_name, + cellid=None) self.trait_list.append((trait_ob, dataset_ob)) #print("trait_list:", self.trait_list) diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index e8b7b057..aa39bc5c 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -82,8 +82,8 @@ class CorrelationResults: dataset_name="Temp", dataset_type="Temp", group_name = start_vars['group']) self.trait_id = start_vars['trait_id'] self.this_trait = create_trait(dataset=self.dataset, - name=self.trait_id, - cellid=None) + name=self.trait_id, + cellid=None) else: helper_functions.get_species_dataset_trait(self, start_vars) @@ -98,7 +98,7 @@ class CorrelationResults: if ('loc_chr' in start_vars and 'min_loc_mb' in start_vars - and 'max_loc_mb' in start_vars): + and 'max_loc_mb' in start_vars): self.location_type = get_string(start_vars, 'location_type') self.location_chr = get_string(start_vars, 'loc_chr') @@ -129,7 +129,7 @@ class CorrelationResults: if corr_samples_group != 'samples_primary': if corr_samples_group == 'samples_other': primary_samples = [x for x in primary_samples if x not in ( - self.dataset.group.parlist + self.dataset.group.f1list)] + self.dataset.group.parlist + self.dataset.group.f1list)] self.process_samples(start_vars, list( self.this_trait.data.keys()), primary_samples) @@ -201,7 +201,7 @@ class CorrelationResults: chr_as_int = order_id if (float(self.correlation_data[trait][0]) >= self.p_range_lower - and float(self.correlation_data[trait][0]) <= self.p_range_upper): + and float(self.correlation_data[trait][0]) <= self.p_range_upper): if (self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Publish") and bool(trait_object.mean): if (self.min_expr != None) and (float(trait_object.mean) < self.min_expr): @@ -221,8 +221,8 @@ class CorrelationResults: continue (trait_object.sample_r, - trait_object.sample_p, - trait_object.num_overlap) = self.correlation_data[trait] + trait_object.sample_p, + trait_object.num_overlap) = self.correlation_data[trait] # Set some sane defaults trait_object.tissue_corr = 0 @@ -277,7 +277,7 @@ class CorrelationResults: trait.symbol for trait in self.correlation_results if trait.symbol] corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( - symbol_list=gene_symbol_list) + symbol_list=gene_symbol_list) for trait in self.correlation_results: if trait.symbol and trait.symbol.lower() in corr_result_tissue_vals_dict: @@ -285,8 +285,8 @@ class CorrelationResults: )] result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values, - this_trait_tissue_values, - self.corr_method) + this_trait_tissue_values, + self.corr_method) trait.tissue_corr = result[0] trait.tissue_pvalue = result[2] @@ -302,7 +302,7 @@ class CorrelationResults: #print("trait_gene_symbols: ", pf(trait_gene_symbols.values())) corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( - symbol_list=list(self.trait_symbol_dict.values())) + symbol_list=list(self.trait_symbol_dict.values())) #print("corr_result_tissue_vals: ", pf(corr_result_tissue_vals_dict)) @@ -315,13 +315,13 @@ class CorrelationResults: )] result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values, - this_trait_tissue_values, - self.corr_method) + this_trait_tissue_values, + self.corr_method) tissue_corr_data[trait] = [symbol, result[0], result[2]] tissue_corr_data = collections.OrderedDict(sorted(list(tissue_corr_data.items()), - key=lambda t: -abs(t[1][1]))) + key=lambda t: -abs(t[1][1]))) return tissue_corr_data @@ -397,7 +397,7 @@ class CorrelationResults: lit_corr_data[trait] = [gene_id, 0] lit_corr_data = collections.OrderedDict(sorted(list(lit_corr_data.items()), - key=lambda t: -abs(t[1][1]))) + key=lambda t: -abs(t[1][1]))) return lit_corr_data @@ -603,12 +603,12 @@ def get_header_fields(data_type, corr_method): if data_type == "ProbeSet": if corr_method == "spearman": header_fields = ['Index', - 'Record', - 'Symbol', - 'Description', - 'Location', - 'Mean', - 'Sample rho', + 'Record', + 'Symbol', + 'Description', + 'Location', + 'Mean', + 'Sample rho', 'N', 'Sample p(rho)', 'Lit rho', @@ -619,12 +619,12 @@ def get_header_fields(data_type, corr_method): 'Additive Effect'] else: header_fields = ['Index', - 'Record', - 'Symbol', - 'Description', - 'Location', - 'Mean', - 'Sample r', + 'Record', + 'Symbol', + 'Description', + 'Location', + 'Mean', + 'Sample r', 'N', 'Sample p(r)', 'Lit r', @@ -636,47 +636,47 @@ def get_header_fields(data_type, corr_method): elif data_type == "Publish": if corr_method == "spearman": header_fields = ['Index', - 'Record', - 'Abbreviation', - 'Description', - 'Mean', - 'Authors', - 'Year', - 'Sample rho', - 'N', - 'Sample p(rho)', - 'Max LRS', - 'Max LRS Location', - 'Additive Effect'] + 'Record', + 'Abbreviation', + 'Description', + 'Mean', + 'Authors', + 'Year', + 'Sample rho', + 'N', + 'Sample p(rho)', + 'Max LRS', + 'Max LRS Location', + 'Additive Effect'] else: header_fields = ['Index', - 'Record', - 'Abbreviation', - 'Description', - 'Mean', - 'Authors', - 'Year', - 'Sample r', - 'N', - 'Sample p(r)', - 'Max LRS', - 'Max LRS Location', - 'Additive Effect'] + 'Record', + 'Abbreviation', + 'Description', + 'Mean', + 'Authors', + 'Year', + 'Sample r', + 'N', + 'Sample p(r)', + 'Max LRS', + 'Max LRS Location', + 'Additive Effect'] else: if corr_method == "spearman": header_fields = ['Index', - 'ID', - 'Location', - 'Sample rho', - 'N', - 'Sample p(rho)'] + 'ID', + 'Location', + 'Sample rho', + 'N', + 'Sample p(rho)'] else: header_fields = ['Index', - 'ID', - 'Location', - 'Sample r', - 'N', - 'Sample p(r)'] + 'ID', + 'Location', + 'Sample r', + 'N', + 'Sample p(r)'] return header_fields diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index c04b17be..c1bf3daa 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -45,7 +45,7 @@ class CorrelationMatrix: def __init__(self, start_vars): trait_db_list = [trait.strip() - for trait in start_vars['trait_list'].split(',')] + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) @@ -215,7 +215,7 @@ class CorrelationMatrix: temp_dataset.group.get_samplelist() for i, pca_trait in enumerate(pca_traits): trait_id = "PCA" + str(i + 1) + "_" + temp_dataset.group.species + "_" + \ - this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S") + this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S") this_vals_string = "" position = 0 for sample in temp_dataset.group.all_samples_ordered(): diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index 820e81bc..a0fb34d8 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -66,12 +66,12 @@ class CTL: def addNode(self, gt): node_dict = {'data': {'id': str(gt.name) + ":" + str(gt.dataset.name), - 'sid': str(gt.name), - 'dataset': str(gt.dataset.name), - 'label': gt.name, - 'symbol': gt.symbol, - 'geneid': gt.geneid, - 'omim': gt.omim}} + 'sid': str(gt.name), + 'dataset': str(gt.dataset.name), + 'label': gt.name, + 'symbol': gt.symbol, + 'geneid': gt.geneid, + 'omim': gt.omim}} self.nodes_list.append(node_dict) def addEdge(self, gtS, gtT, significant, x): @@ -87,7 +87,7 @@ class CTL: def run_analysis(self, requestform): logger.info("Starting CTL analysis on dataset") self.trait_db_list = [trait.strip() - for trait in requestform['trait_list'].split(',')] + for trait in requestform['trait_list'].split(',')] self.trait_db_list = [x for x in self.trait_db_list if x] logger.debug("strategy:", requestform.get("strategy")) @@ -179,9 +179,9 @@ class CTL: for trait in self.trait_db_list: # Create the QTL like CTL plots self.results['imgurl' + \ - str(n)] = webqtlUtil.genRandStr("CTL_") + ".png" + str(n)] = webqtlUtil.genRandStr("CTL_") + ".png" self.results['imgloc' + str(n)] = GENERATED_IMAGE_DIR + \ - self.results['imgurl' + str(n)] + self.results['imgurl' + str(n)] r_png(self.results['imgloc' + str(n)], width=1000, height=600, type='cairo-png') self.r_plotCTLobject( diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 48527785..761ae326 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -112,7 +112,7 @@ class MrnaAssaySearch(DoSearch): match_clause = "" where_clause = (match_clause - + """ProbeSet.Id = ProbeSetXRef.ProbeSetId + + """ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId = %s """ % (escape(str(self.dataset.id)))) @@ -135,7 +135,7 @@ class MrnaAssaySearch(DoSearch): match_clause = "" where_clause = (match_clause - + """ProbeSet.Id = ProbeSetXRef.ProbeSetId + + """ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId = %s """ % (escape(str(self.dataset.id)))) @@ -147,14 +147,14 @@ class MrnaAssaySearch(DoSearch): from_clause = self.normalize_spaces(from_clause) query = (self.base_query + - """%s + """%s WHERE %s and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId = %s ORDER BY ProbeSet.symbol ASC """ % (escape(from_clause), - where_clause, - escape(str(self.dataset.id)))) + where_clause, + escape(str(self.dataset.id)))) return query def run_combined(self, from_clause='', where_clause=''): @@ -166,14 +166,14 @@ class MrnaAssaySearch(DoSearch): from_clause = self.normalize_spaces(from_clause) query = (self.base_query + - """%s + """%s WHERE %s and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId = %s ORDER BY ProbeSet.symbol ASC """ % (escape(from_clause), - where_clause, - escape(str(self.dataset.id)))) + where_clause, + escape(str(self.dataset.id)))) return self.execute(query) @@ -199,15 +199,15 @@ class PhenotypeSearch(DoSearch): FROM Phenotype, PublishFreeze, Publication, PublishXRef """ search_fields = ('Phenotype.Post_publication_description', - 'Phenotype.Pre_publication_description', - 'Phenotype.Pre_publication_abbreviation', - 'Phenotype.Post_publication_abbreviation', - 'Phenotype.Lab_code', - 'Publication.PubMed_ID', - 'Publication.Abstract', - 'Publication.Title', - 'Publication.Authors', - 'PublishXRef.Id') + 'Phenotype.Pre_publication_description', + 'Phenotype.Pre_publication_abbreviation', + 'Phenotype.Post_publication_abbreviation', + 'Phenotype.Lab_code', + 'Publication.PubMed_ID', + 'Publication.Abstract', + 'Publication.Title', + 'Publication.Authors', + 'PublishXRef.Id') header_fields = ['Index', 'Record', @@ -250,28 +250,28 @@ class PhenotypeSearch(DoSearch): if self.search_term[0] == "*": query = (self.base_query + - """%s + """%s WHERE PublishXRef.InbredSetId = %s and PublishXRef.PhenotypeId = Phenotype.Id and PublishXRef.PublicationId = Publication.Id and PublishFreeze.Id = %s ORDER BY PublishXRef.Id""" % ( - from_clause, - escape(str(self.dataset.group.id)), - escape(str(self.dataset.id)))) + from_clause, + escape(str(self.dataset.group.id)), + escape(str(self.dataset.id)))) else: query = (self.base_query + - """%s + """%s WHERE %s and PublishXRef.InbredSetId = %s and PublishXRef.PhenotypeId = Phenotype.Id and PublishXRef.PublicationId = Publication.Id and PublishFreeze.Id = %s ORDER BY PublishXRef.Id""" % ( - from_clause, - where_clause, - escape(str(self.dataset.group.id)), - escape(str(self.dataset.id)))) + from_clause, + where_clause, + escape(str(self.dataset.group.id)), + escape(str(self.dataset.id)))) return query @@ -283,16 +283,16 @@ class PhenotypeSearch(DoSearch): from_clause = self.normalize_spaces(from_clause) query = (self.base_query + - """%s + """%s WHERE %s PublishXRef.InbredSetId = %s and PublishXRef.PhenotypeId = Phenotype.Id and PublishXRef.PublicationId = Publication.Id and PublishFreeze.Id = %s""" % ( - from_clause, - where_clause, - escape(str(self.dataset.group.id)), - escape(str(self.dataset.id)))) + from_clause, + where_clause, + escape(str(self.dataset.group.id)), + escape(str(self.dataset.id)))) return self.execute(query) @@ -336,7 +336,7 @@ class GenotypeSearch(DoSearch): for field in self.search_fields: where_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % self.mescape(self.dataset.type, field), - self.search_term)) + self.search_term)) logger.debug("hello ;where_clause is:", pf(where_clause)) where_clause = "(%s) " % ' OR '.join(where_clause) @@ -349,16 +349,16 @@ class GenotypeSearch(DoSearch): if self.search_term[0] == "*": query = (self.base_query - + """WHERE Geno.Id = GenoXRef.GenoId + + """WHERE Geno.Id = GenoXRef.GenoId and GenoXRef.GenoFreezeId = GenoFreeze.Id and GenoFreeze.Id = %s""" % (escape(str(self.dataset.id)))) else: query = (self.base_query + - """WHERE %s + """WHERE %s and Geno.Id = GenoXRef.GenoId and GenoXRef.GenoFreezeId = GenoFreeze.Id and GenoFreeze.Id = %s""" % (where_clause, - escape(str(self.dataset.id)))) + escape(str(self.dataset.id)))) return query @@ -526,7 +526,7 @@ class LrsSearch(DoSearch): where_clause += """ and %sXRef.Locus = Geno.name and Geno.SpeciesId = %s """ % self.mescape(self.dataset.type, - self.species_id) + self.species_id) else: # Deal with >, <, >=, and <= logger.debug("self.search_term is:", self.search_term) @@ -535,8 +535,8 @@ class LrsSearch(DoSearch): lrs_val = lrs_val * 4.61 where_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type, - self.search_operator, - self.search_term[0]) + self.search_operator, + self.search_term[0]) return where_clause @@ -618,18 +618,18 @@ class CisTransLrsSearch(DoSearch): sub_clause = """ %sXRef.LRS > %s and %sXRef.LRS < %s and """ % ( - escape(self.dataset.type), - escape(str(min(lrs_min, lrs_max))), - escape(self.dataset.type), - escape(str(max(lrs_min, lrs_max))) - ) + escape(self.dataset.type), + escape(str(min(lrs_min, lrs_max))), + escape(self.dataset.type), + escape(str(max(lrs_min, lrs_max))) + ) else: # Deal with >, <, >=, and <= sub_clause = """ %sXRef.LRS %s %s and """ % ( - escape(self.dataset.type), - escape(self.search_operator), - escape(self.search_term[0]) - ) + escape(self.dataset.type), + escape(self.search_operator), + escape(self.search_term[0]) + ) if cis_trans == "cis": where_clause = sub_clause + """ @@ -637,27 +637,27 @@ class CisTransLrsSearch(DoSearch): %sXRef.Locus = Geno.name and Geno.SpeciesId = %s and %s.Chr = Geno.Chr""" % ( - escape(self.dataset.type), - the_operator, - escape(str(self.mb_buffer)), - escape(self.dataset.type), - escape(str(self.species_id)), - escape(self.dataset.type) - ) + escape(self.dataset.type), + the_operator, + escape(str(self.mb_buffer)), + escape(self.dataset.type), + escape(str(self.species_id)), + escape(self.dataset.type) + ) else: if chromosome: location_clause = "(%s.Chr = '%s' and %s.Chr = Geno.Chr and ABS(%s.Mb-Geno.Mb) %s %s) or (%s.Chr != Geno.Chr and Geno.Chr = '%s')" % (escape(self.dataset.type), - chromosome, - escape( + chromosome, + escape( self.dataset.type), - escape( + escape( self.dataset.type), - the_operator, - escape( + the_operator, + escape( str(self.mb_buffer)), - escape( + escape( self.dataset.type), - chromosome) + chromosome) else: location_clause = "(ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or (%s.Chr != Geno.Chr)" % (escape( self.dataset.type), the_operator, escape(str(self.mb_buffer)), escape(self.dataset.type), escape(self.dataset.type)) @@ -665,10 +665,10 @@ class CisTransLrsSearch(DoSearch): %sXRef.Locus = Geno.name and Geno.SpeciesId = %s and (%s)""" % ( - escape(self.dataset.type), - escape(str(self.species_id)), - location_clause - ) + escape(self.dataset.type), + escape(str(self.species_id)), + location_clause + ) return where_clause @@ -752,15 +752,15 @@ class MeanSearch(MrnaAssaySearch): where_clause = """ %sXRef.mean > %s and %sXRef.mean < %s """ % self.mescape(self.dataset.type, - min(self.mean_min, - self.mean_max), - self.dataset.type, - max(self.mean_min, self.mean_max)) + min(self.mean_min, + self.mean_max), + self.dataset.type, + max(self.mean_min, self.mean_max)) else: # Deal with >, <, >=, and <= where_clause = """ %sXRef.mean %s %s """ % self.mescape(self.dataset.type, - self.search_operator, - self.search_term[0]) + self.search_operator, + self.search_term[0]) return where_clause @@ -893,17 +893,17 @@ class PvalueSearch(MrnaAssaySearch): self.pvalue_min, self.pvalue_max = self.search_term[:2] self.where_clause = """ %sXRef.pValue > %s and %sXRef.pValue < %s """ % self.mescape( - self.dataset.type, - min(self.pvalue_min, self.pvalue_max), - self.dataset.type, - max(self.pvalue_min, self.pvalue_max)) + self.dataset.type, + min(self.pvalue_min, self.pvalue_max), + self.dataset.type, + max(self.pvalue_min, self.pvalue_max)) else: # Deal with >, <, >=, and <= self.where_clause = """ %sXRef.pValue %s %s """ % self.mescape( - self.dataset.type, - self.search_operator, - self.search_term[0]) + self.dataset.type, + self.search_operator, + self.search_term[0]) logger.debug("where_clause is:", pf(self.where_clause)) diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py index 2c180d49..a22d6acc 100644 --- a/wqflask/wqflask/export_traits.py +++ b/wqflask/wqflask/export_traits.py @@ -60,7 +60,7 @@ def export_search_results_csv(targs): trait_list.append(trait_ob) table_headers = ['Index', 'URL', 'Species', 'Group', 'Dataset', 'Record ID', 'Symbol', 'Description', 'ProbeTarget', 'PubMed_ID', 'Chr', 'Mb', 'Alias', 'Gene_ID', 'Homologene_ID', 'UniGene_ID', - 'Strand_Probe', 'Probe_set_specificity', 'Probe_set_BLAT_score', 'Probe_set_BLAT_Mb_start', 'Probe_set_BLAT_Mb_end', 'QTL_Chr', 'QTL_Mb', 'Locus_at_Peak', 'Max_LRS', 'P_value_of_MAX', 'Mean_Expression'] + 'Strand_Probe', 'Probe_set_specificity', 'Probe_set_BLAT_score', 'Probe_set_BLAT_Mb_start', 'Probe_set_BLAT_Mb_end', 'QTL_Chr', 'QTL_Mb', 'Locus_at_Peak', 'Max_LRS', 'P_value_of_MAX', 'Mean_Expression'] traits_by_group = sort_traits_by_group(trait_list) @@ -93,7 +93,7 @@ def export_search_results_csv(targs): row_contents = [ i + 1, "https://genenetwork.org/show_trait?trait_id=" + \ - str(trait.name) + "&dataset=" + str(trait.dataset.name), + str(trait.name) + "&dataset=" + str(trait.dataset.name), trait.dataset.group.species, trait.dataset.group.name, trait.dataset.name, @@ -124,7 +124,7 @@ def export_search_results_csv(targs): for sample in trait.dataset.group.samplelist: if sample in trait.data: row_contents += [trait.data[sample].value, - trait.data[sample].variance] + trait.data[sample].variance] else: row_contents += ["x", "x"] diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py index 3c0f2ca7..c1b14ede 100644 --- a/wqflask/wqflask/external_tools/send_to_bnw.py +++ b/wqflask/wqflask/external_tools/send_to_bnw.py @@ -28,7 +28,7 @@ logger = utility.logger.getLogger(__name__) class SendToBNW: def __init__(self, start_vars): trait_db_list = [trait.strip() - for trait in start_vars['trait_list'].split(',')] + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) trait_samples_list = [] diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py index 8af9bee9..9a4f7150 100644 --- a/wqflask/wqflask/external_tools/send_to_geneweaver.py +++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py @@ -33,7 +33,7 @@ logger = utility.logger.getLogger(__name__) class SendToGeneWeaver: def __init__(self, start_vars): trait_db_list = [trait.strip() - for trait in start_vars['trait_list'].split(',')] + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) self.chip_name = test_chip(self.trait_list) @@ -54,11 +54,11 @@ class SendToGeneWeaver: trait_name_list = get_trait_name_list(self.trait_list) self.hidden_vars = { - 'client': "genenetwork", - 'species': species_name, - 'idtype': self.chip_name, - 'list': ",".join(trait_name_list), - } + 'client': "genenetwork", + 'species': species_name, + 'idtype': self.chip_name, + 'list': ",".join(trait_name_list), + } def get_trait_name_list(trait_list): diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py index fcd943ba..6e74f4fe 100644 --- a/wqflask/wqflask/external_tools/send_to_webgestalt.py +++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py @@ -33,7 +33,7 @@ logger = utility.logger.getLogger(__name__) class SendToWebGestalt: def __init__(self, start_vars): trait_db_list = [trait.strip() - for trait in start_vars['trait_list'].split(',')] + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) self.chip_name = test_chip(self.trait_list) @@ -49,7 +49,7 @@ class SendToWebGestalt: id_type = "entrezgene" self.hidden_vars = { - 'gene_list': "\n".join(gene_id_list), + 'gene_list': "\n".join(gene_id_list), 'id_type': "entrezgene", 'ref_set': "genome", 'enriched_database_category': "geneontology", @@ -59,7 +59,7 @@ class SendToWebGestalt: 'enrich_method': "ORA", 'fdr_method': "BH", 'min_num': "2" - } + } species = self.trait_list[0][1].group.species if species == "rat": diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py index 995915a9..b7e7e38a 100644 --- a/wqflask/wqflask/group_manager.py +++ b/wqflask/wqflask/group_manager.py @@ -8,7 +8,7 @@ from wqflask import app from wqflask.user_login import send_verification_email, send_invitation_email, basic_info, set_password from utility.redis_tools import get_user_groups, get_group_info, save_user, create_group, delete_group, add_users_to_group, remove_users_from_group, \ - change_group_name, save_verification_code, check_verification_code, get_user_by_unique_column, get_resources, get_resource_info + change_group_name, save_verification_code, check_verification_code, get_user_by_unique_column, get_resources, get_resource_info from utility.logger import getLogger logger = getLogger(__name__) @@ -78,9 +78,9 @@ def remove_users(): member_ids_to_remove = request.form['selected_member_ids'] remove_users_from_group(g.user_session.user_id, admin_ids_to_remove.split( - ":"), group_id, user_type="admins") + ":"), group_id, user_type="admins") remove_users_from_group(g.user_session.user_id, member_ids_to_remove.split( - ":"), group_id, user_type="members") + ":"), group_id, user_type="members") return redirect(url_for('view_group', id=group_id)) @@ -133,7 +133,7 @@ def add_or_edit_group(): #send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members") create_group(list(admin_user_ids), list( - member_user_ids), params['group_name']) + member_user_ids), params['group_name']) return redirect(url_for('manage_groups')) else: return render_template("admin/create_group.html") @@ -159,13 +159,13 @@ def send_group_invites(group_id, user_email_list=[], user_type="members"): key_prefix="verification_code", subject = "You've been invited to join a GeneNetwork user group") else: temp_password = ''.join(random.choice( - string.ascii_uppercase + string.digits) for _ in range(6)) + string.ascii_uppercase + string.digits) for _ in range(6)) user_details = { - 'user_id': str(uuid.uuid4()), - 'email_address': user_email, - 'registration_info': basic_info(), - 'password': set_password(temp_password), - 'confirmed': 0 + 'user_id': str(uuid.uuid4()), + 'email_address': user_email, + 'registration_info': basic_info(), + 'password': set_password(temp_password), + 'confirmed': 0 } save_user(user_details, user_details['user_id']) send_invitation_email(user_email, temp_password) diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index f02da27c..fb8bdc55 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -124,7 +124,7 @@ class GSearch: if this_trait['locus_chr'] != None and this_trait['locus_mb'] != None: max_lrs_text = "Chr" + \ str(this_trait['locus_chr']) + \ - ": " + str(this_trait['locus_mb']) + ": " + str(this_trait['locus_mb']) this_trait['max_lrs_text'] = max_lrs_text trait_list.append(this_trait) @@ -133,18 +133,18 @@ class GSearch: self.trait_list = json.dumps(trait_list) self.header_fields = ['Index', - 'Record', - 'Species', - 'Group', - 'Tissue', - 'Dataset', - 'Symbol', - 'Description', - 'Location', - 'Mean', - 'Max LRS', - 'Max LRS Location', - 'Additive Effect'] + 'Record', + 'Species', + 'Group', + 'Tissue', + 'Dataset', + 'Symbol', + 'Description', + 'Location', + 'Mean', + 'Max LRS', + 'Max LRS Location', + 'Additive Effect'] elif self.type == "phenotype": search_term = self.terms @@ -251,7 +251,7 @@ class GSearch: if trait_ob.locus_chr != "" and trait_ob.locus_mb != "": this_trait['max_lrs_text'] = "Chr" + \ str(trait_ob.locus_chr) + \ - ": " + str(trait_ob.locus_mb) + ": " + str(trait_ob.locus_mb) except: this_trait['max_lrs_text'] = "N/A" @@ -261,12 +261,12 @@ class GSearch: self.trait_list = json.dumps(trait_list) self.header_fields = ['Index', - 'Species', - 'Group', - 'Record', - 'Description', - 'Authors', - 'Year', - 'Max LRS', - 'Max LRS Location', - 'Additive Effect'] + 'Species', + 'Group', + 'Record', + 'Description', + 'Authors', + 'Year', + 'Max LRS', + 'Max LRS Location', + 'Additive Effect'] diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 02eb66e5..001bab3b 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -19,7 +19,7 @@ class Heatmap: def __init__(self, start_vars, temp_uuid): trait_db_list = [trait.strip() - for trait in start_vars['trait_list'].split(',')] + for trait in start_vars['trait_list'].split(',')] helper_functions.get_trait_db_obs(self, trait_db_list) self.temp_uuid = temp_uuid @@ -35,7 +35,7 @@ class Heatmap: self.species = species.TheSpecies(dataset=self.trait_list[0][1]) for key in list(self.species.chromosomes.chromosomes.keys()): chrnames.append([self.species.chromosomes.chromosomes[key].name, - self.species.chromosomes.chromosomes[key].mb_length]) + self.species.chromosomes.chromosomes[key].mb_length]) for trait_db in self.trait_list: @@ -111,7 +111,7 @@ class Heatmap: trimmed_values.append(values[i]) trait_filename = str(this_trait.name) + "_" + \ - str(self.dataset.name) + "_pheno" + str(self.dataset.name) + "_pheno" gen_pheno_txt_file(trimmed_samples, trimmed_values, trait_filename) output_filename = self.dataset.group.name + "_GWA_" + \ @@ -119,11 +119,11 @@ class Heatmap: for _ in range(6)) reaper_command = REAPER_COMMAND + ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt -n 1000 -o {4}{5}.txt'.format(flat_files('genotype'), - genofile_name, - TEMPDIR, - trait_filename, - webqtlConfig.GENERATED_IMAGE_DIR, - output_filename) + genofile_name, + TEMPDIR, + trait_filename, + webqtlConfig.GENERATED_IMAGE_DIR, + output_filename) os.system(reaper_command) diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py index 2f1c142c..04980281 100644 --- a/wqflask/wqflask/interval_analyst/GeneUtil.py +++ b/wqflask/wqflask/interval_analyst/GeneUtil.py @@ -8,8 +8,8 @@ from flask import Flask, g def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd', - 'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID', - 'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd'] + 'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID', + 'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd'] # List All Species in the Gene Table speciesDict = {} @@ -34,9 +34,9 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): ((TxStart > %f and TxStart <= %f) OR (TxEnd > %f and TxEnd <= %f)) ORDER BY txStart """ % (", ".join(fetchFields), - speciesId, chrName, - startMb, endMb, - startMb, endMb)).fetchall() + speciesId, chrName, + startMb, endMb, + startMb, endMb)).fetchall() GeneList = [] @@ -55,7 +55,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): StrainId1 = %d AND StrainId2 = %d """ % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1])).fetchone()[0] newdict["snpDensity"] = newdict["snpCount"] / \ - (newdict["TxEnd"] - newdict["TxStart"]) / 1000.0 + (newdict["TxEnd"] - newdict["TxStart"]) / 1000.0 else: newdict["snpDensity"] = newdict["snpCount"] = 0 @@ -70,8 +70,8 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): newdict2 = {} resultsOther = g.db.execute("SELECT %s FROM GeneList WHERE SpeciesId = %d AND geneSymbol= '%s' LIMIT 1" % (", ".join(fetchFields), - othSpecId, - newdict["GeneSymbol"])).fetchone() + othSpecId, + newdict["GeneSymbol"])).fetchone() if resultsOther: for j, item in enumerate(fetchFields): @@ -88,13 +88,13 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'): """ % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1])).fetchone()[0] newdict2["snpDensity"] = newdict2["snpCount"] / \ - (newdict2["TxEnd"] - newdict2["TxStart"]) / 1000.0 + (newdict2["TxEnd"] - newdict2["TxStart"]) / 1000.0 else: newdict2["snpDensity"] = newdict2["snpCount"] = 0 try: newdict2['GeneLength'] = 1000.0 * \ - (newdict2['TxEnd'] - newdict2['TxStart']) + (newdict2['TxEnd'] - newdict2['TxStart']) except: pass diff --git a/wqflask/wqflask/markdown_routes.py b/wqflask/wqflask/markdown_routes.py index ebf75807..c27ff143 100644 --- a/wqflask/wqflask/markdown_routes.py +++ b/wqflask/wqflask/markdown_routes.py @@ -103,7 +103,7 @@ def environments(): @environments_blueprint.route('/svg-dependency-graph') def svg_graph(): directory, file_name, _ = get_file_from_python_search_path( - "wqflask/dependency-graph.svg").partition("dependency-graph.svg") + "wqflask/dependency-graph.svg").partition("dependency-graph.svg") return send_from_directory(directory, file_name) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index c68e0fde..f3b1b1fc 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -629,7 +629,7 @@ class DisplayMappingResults: submit=HtmlGenWrapper.create_input_tag(type_='hidden')) hddn = {'FormID': 'showDatabase', 'ProbeSetID': '_', 'database': fd.RISet+ \ - "Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'} + "Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'} for key in hddn.keys(): showLocusForm.append(HtmlGenWrapper.create_input_tag( name=key, value=hddn[key], type_='hidden')) @@ -889,7 +889,7 @@ class DisplayMappingResults: bootY = yZero - bootHeightThresh * item / highestPercent im_drawer.line( xy=((canvas.size[0] - bootOffset + 4, bootY), - (canvas.size[0] - bootOffset, bootY)), + (canvas.size[0] - bootOffset, bootY)), fill=BLACK) im_drawer.text(xy=(canvas.size[0] - bootOffset + 10, bootY+TEXT_Y_DISPLACEMENT), text='%2.1f' % item, font=bootScaleFont, fill=BLACK) @@ -983,7 +983,7 @@ class DisplayMappingResults: break if locPixel >= 0 and self.plotScale == 'physic': traitPixel = ((locPixel, yZero), (locPixel - 7, - yZero + 14), (locPixel + 7, yZero + 14)) + yZero + 14), (locPixel + 7, yZero + 14)) draw_open_polygon(canvas, xy=traitPixel, outline=BLACK, fill=self.TRANSCRIPT_LOCATION_COLOR) @@ -1029,7 +1029,7 @@ class DisplayMappingResults: SNPCounts[i - xLeftOffset] * SNP_HEIGHT_MODIFIER / maxCount) im_drawer.line( xy=((i, drawSNPLocationY + (snpDensity) * zoom), - (i, drawSNPLocationY - (snpDensity) * zoom)), + (i, drawSNPLocationY - (snpDensity) * zoom)), fill=self.SNP_COLOR, width=1) def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset=(40, 120, 80, 10), zoom=1): @@ -1356,7 +1356,7 @@ class DisplayMappingResults: # always apply colors now, even if SNP Track not checked - Zach 11/24/2010 densities = [1.0000000000000001e-05, 0.094094033555233408, - 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0] + 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0] if SNPdensity < densities[0]: myColor = BLACK elif SNPdensity < densities[1]: @@ -1462,13 +1462,13 @@ class DisplayMappingResults: xy=((geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, geneYLocation), (geneStartPix + xCoord, - geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)), + geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)), fill=arrowColor, width=1) im_drawer.line( xy=((geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH, geneYLocation + self.EACH_GENE_HEIGHT * zoom), (geneStartPix + xCoord, - geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)), + geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)), fill=arrowColor, width=1) # draw the blocks for the exon regions @@ -1476,7 +1476,7 @@ class DisplayMappingResults: exonStartPix = ( exonStarts[i] - startMb) * plotXScale + xLeftOffset exonEndPix = (exonEnds[i] - startMb) * \ - plotXScale + xLeftOffset + plotXScale + xLeftOffset if (exonStartPix < xLeftOffset): exonStartPix = xLeftOffset if (exonEndPix < xLeftOffset): @@ -1493,7 +1493,7 @@ class DisplayMappingResults: # draw gray blocks for 3' and 5' UTR blocks if cdsStart and cdsEnd: utrStartPix = (txStart - startMb) * \ - plotXScale + xLeftOffset + plotXScale + xLeftOffset utrEndPix = (cdsStart - startMb) * plotXScale + xLeftOffset if (utrStartPix < xLeftOffset): utrStartPix = xLeftOffset @@ -1741,9 +1741,9 @@ class DisplayMappingResults: mylineColor = self.HAPLOTYPE_RECOMBINATION im_drawer.line( xy=((plotRight, - geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom), + geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom), (drawEnd, - geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom)), + geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom)), fill= mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2)) if lastGene == 0: @@ -1869,7 +1869,7 @@ class DisplayMappingResults: fill=self.CLICKABLE_WEBQTL_REGION_COLOR) im_drawer.line( xy=((xBrowse1, paddingTop), (xBrowse1, - (paddingTop + self.BAND_HEIGHT))), + (paddingTop + self.BAND_HEIGHT))), fill=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR) if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat": @@ -1895,7 +1895,7 @@ class DisplayMappingResults: fill=self.CLICKABLE_PHENOGEN_REGION_COLOR) im_drawer.line( xy=((xBrowse1, phenogenPaddingTop), (xBrowse1, - (phenogenPaddingTop + self.BAND_HEIGHT))), + (phenogenPaddingTop + self.BAND_HEIGHT))), fill=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR) UCSC_COORDS = "%d, %d, %d, %d" % ( @@ -2051,7 +2051,7 @@ class DisplayMappingResults: fill=xAxisLabelColor) else: im_drawer.line(xy=((Xc, yZero), - (Xc, yZero + xMinorTickHeight)), + (Xc, yZero + xMinorTickHeight)), fill=xAxisTickMarkColor, width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark @@ -2159,17 +2159,17 @@ class DisplayMappingResults: if differ: im_drawer.line( xy=((startPosX + Lpos, yZero), (xLeftOffset + offsetA,\ - yZero + 25)), + yZero + 25)), fill=lineColor) im_drawer.line( xy=((xLeftOffset + offsetA, yZero + 25), (xLeftOffset+offsetA,\ - yZero + 40 + Zorder*(LRectWidth+3))), + yZero + 40 + Zorder*(LRectWidth+3))), fill=lineColor) rectColor = ORANGE else: im_drawer.line( xy=((xLeftOffset + offsetA, yZero + 40+Zorder*(LRectWidth+3)-3), (\ - xLeftOffset + offsetA, yZero + 40+Zorder*(LRectWidth+3))), + xLeftOffset + offsetA, yZero + 40+Zorder*(LRectWidth+3))), fill=lineColor) rectColor = DEEPPINK im_drawer.rectangle( @@ -2178,7 +2178,7 @@ class DisplayMappingResults: yZero + 40 + Zorder*(LRectWidth+3)+LRectWidth)), outline=rectColor, fill=rectColor, width=0) COORDS = "%d,%d,%d,%d" % (xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\ - xLeftOffset + offsetA, yZero +40+Zorder*(LRectWidth+3)+LRectWidth) + xLeftOffset + offsetA, yZero +40+Zorder*(LRectWidth+3)+LRectWidth) HREF = "/show_trait?trait_id=%s&dataset=%s" % ( Lname, self.dataset.group.name + "Geno") #HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname) @@ -2230,7 +2230,7 @@ class DisplayMappingResults: if self.lrsMax <= 0: # sliding scale if "lrs_value" in self.qtlresults[0]: LRS_LOD_Max = max([result['lrs_value'] - for result in self.qtlresults]) + for result in self.qtlresults]) if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP": LRS_LOD_Max = LRS_LOD_Max / self.LODFACTOR if self.permChecked and self.nperm > 0 and not self.multipleInterval: @@ -2248,7 +2248,7 @@ class DisplayMappingResults: pass else: LRS_LOD_Max = max([result['lod_score'] - for result in self.qtlresults]) + for result in self.qtlresults]) if self.LRS_LOD == "LRS": LRS_LOD_Max = LRS_LOD_Max * self.LODFACTOR if self.permChecked and self.nperm > 0 and not self.multipleInterval: @@ -2390,7 +2390,7 @@ class DisplayMappingResults: ) im_drawer.line( xy=((start_pos_x + self.SUGGESTIVE_WIDTH / 1.5, significantY), - (rightEdge, significantY)), + (rightEdge, significantY)), fill=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH * zoom # , clipX=(xLeftOffset, xLeftOffset + plotWidth-2) @@ -2440,7 +2440,7 @@ class DisplayMappingResults: else: if self.additiveChecked: additiveMax = max([abs(X['additive']) - for X in self.qtlresults]) + for X in self.qtlresults]) lrsEdgeWidth = 3 if zoom == 2: @@ -2484,7 +2484,7 @@ class DisplayMappingResults: Xcm = Xc else: Xcm = (yZero - Yc0) / \ - ((Yc - Yc0) / (Xc - Xc0)) + Xc0 + ((Yc - Yc0) / (Xc - Xc0)) + Xc0 if Yc0 < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xcm, yZero)), @@ -2583,12 +2583,12 @@ class DisplayMappingResults: #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR) Yc = yZero - webqtlConfig.MAXLRS * \ LRSHeightThresh / \ - (LRS_LOD_Max * self.LODFACTOR) + (LRS_LOD_Max * self.LODFACTOR) else: #Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR) Yc = yZero - \ qtlresult['lrs_value'] * LRSHeightThresh / \ - (LRS_LOD_Max * self.LODFACTOR) + (LRS_LOD_Max * self.LODFACTOR) else: if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf': #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1] @@ -2597,7 +2597,7 @@ class DisplayMappingResults: #Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSAxisList[-1] Yc = yZero - \ qtlresult['lrs_value'] * \ - LRSHeightThresh / LRS_LOD_Max + LRSHeightThresh / LRS_LOD_Max else: if qtlresult['lod_score'] > 100 or qtlresult['lod_score'] == 'inf': #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1] @@ -2607,12 +2607,12 @@ class DisplayMappingResults: #Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRSAxisList[-1] Yc = yZero - \ qtlresult['lod_score'] * self.LODFACTOR * \ - LRSHeightThresh / LRS_LOD_Max + LRSHeightThresh / LRS_LOD_Max else: #Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRSAxisList[-1] Yc = yZero - \ qtlresult['lod_score'] * \ - LRSHeightThresh / LRS_LOD_Max + LRSHeightThresh / LRS_LOD_Max if self.manhattan_plot == True: if self.color_scheme == "single": @@ -2665,7 +2665,7 @@ class DisplayMappingResults: Xcm = Xc else: Xcm = (yZero - Yc0) / \ - ((Yc - Yc0) / (Xc - Xc0)) + Xc0 + ((Yc - Yc0) / (Xc - Xc0)) + Xc0 if Yc0 < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xcm, yZero)), @@ -2731,7 +2731,7 @@ class DisplayMappingResults: Xcm = Xc else: Xcm = (yZero - Yc0) / \ - ((Yc - Yc0) / (Xc - Xc0)) + Xc0 + ((Yc - Yc0) / (Xc - Xc0)) + Xc0 if Yc0 < yZero: im_drawer.line( xy=((Xc0, Yc0), (Xcm, yZero)), @@ -2947,12 +2947,12 @@ class DisplayMappingResults: if self.dataset.group.species == "mouse": if refGene: gene_table_header_list = ["Index", - "Symbol", - "Mb Start", - "Length (Kb)", - "SNP Count", - "SNP Density", - "Avg Expr", + "Symbol", + "Mb Start", + "Length (Kb)", + "SNP Count", + "SNP Density", + "Avg Expr", "Human Chr", "Mb Start (hg19)", "Literature Correlation", diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 9f9591ad..5d16abde 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -26,18 +26,18 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo gen_pheno_txt_file(samples, vals, trait_filename) output_filename = (f"{this_dataset.group.name}_GWA_" - + ''.join(random.choice(string.ascii_uppercase + string.digits) - for _ in range(6)) - ) + + ''.join(random.choice(string.ascii_uppercase + string.digits) + for _ in range(6)) + ) bootstrap_filename = None permu_filename = None opt_list = [] if boot_check and num_bootstrap > 0: bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_" - + ''.join(random.choice(string.ascii_uppercase + string.digits) - for _ in range(6)) - ) + + ''.join(random.choice(string.ascii_uppercase + string.digits) + for _ in range(6)) + ) opt_list.append("-b") opt_list.append(f"--n_bootstrap {str(num_bootstrap)}") @@ -45,8 +45,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo f"--bootstrap_output {webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt") if num_perm > 0: permu_filename = ("{this_dataset.group.name}_PERM_" - + ''.join(random.choice(string.ascii_uppercase - + string.digits) for _ in range(6)) + + ''.join(random.choice(string.ascii_uppercase + + string.digits) for _ in range(6)) ) opt_list.append("-n " + str(num_perm)) opt_list.append( @@ -57,15 +57,15 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo opt_list.append("--interval 1") reaper_command = (REAPER_COMMAND + - ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt {4} -o {5}{6}.txt'.format(flat_files('genotype'), + ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt {4} -o {5}{6}.txt'.format(flat_files('genotype'), - genofile_name, - TEMPDIR, - trait_filename, - " ".join( - opt_list), - webqtlConfig.GENERATED_IMAGE_DIR, - output_filename)) + genofile_name, + TEMPDIR, + trait_filename, + " ".join( + opt_list), + webqtlConfig.GENERATED_IMAGE_DIR, + output_filename)) logger.debug("reaper_command:" + reaper_command) os.system(reaper_command) @@ -82,7 +82,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo significant = permu_vals[int(num_perm * 0.95 - 1)] return (marker_obs, permu_vals, suggestive, significant, bootstrap_vals, - [output_filename, permu_filename, bootstrap_filename]) + [output_filename, permu_filename, bootstrap_filename]) def gen_pheno_txt_file(samples, vals, trait_filename): @@ -231,17 +231,17 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da control_geno.append(control_geno2[_idx]) bootstrap_results = genotype.bootstrap(strains=trimmed_samples, - trait=trimmed_values, - control=control_geno, - nboot=num_bootstrap) + trait=trimmed_values, + control=control_geno, + nboot=num_bootstrap) else: reaper_results = genotype.regression(strains=trimmed_samples, trait=trimmed_values) if bootCheck: bootstrap_results = genotype.bootstrap(strains=trimmed_samples, - trait=trimmed_values, - nboot=num_bootstrap) + trait=trimmed_values, + nboot=num_bootstrap) json_data['chr'] = [] json_data['pos'] = [] @@ -265,7 +265,7 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da # if self.additive: # self.json_data['additive'].append(qtl.additive) locus = {"name": reaper_locus.name, "chr": reaper_locus.chr, - "cM": reaper_locus.cM, "Mb": reaper_locus.Mb} + "cM": reaper_locus.cM, "Mb": reaper_locus.Mb} qtl = {"lrs_value": qtl.lrs, "chr": converted_chr, "Mb": reaper_locus.Mb, "cM": reaper_locus.cM, "name": reaper_locus.name, "additive": qtl.additive, "dominance": qtl.dominance} qtl_results.append(qtl) diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index 32dbad1f..cf8cf514 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -411,7 +411,7 @@ def process_pair_scan_results(result): result = result[1] output = [tuple([result[j][i] for j in range(result.ncol)]) - for i in range(result.nrow)] + for i in range(result.nrow)] for i, line in enumerate(result.iter_row()): marker = {} @@ -441,7 +441,7 @@ def process_rqtl_perm_results(num_perm, results): def process_rqtl_results(result, species_name): qtl_results = [] output = [tuple([result[j][i] for j in range(result.ncol)]) - for i in range(result.nrow)] + for i in range(result.nrow)] for i, line in enumerate(result.iter_row()): marker = {} diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 041f4348..81e0a03f 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -289,18 +289,18 @@ class RunMapping: ",") results, self.perm_output, self.suggestive, self.significant, self.bootstrap_results, self.output_files = qtlreaper_mapping.run_reaper(self.this_trait, - self.dataset, - self.samples, - self.vals, - self.json_data, - self.num_perm, - self.bootCheck, - self.num_bootstrap, - self.do_control, - self.control_marker, - self.manhattan_plot, - self.first_run, - self.output_files) + self.dataset, + self.samples, + self.vals, + self.json_data, + self.num_perm, + self.bootCheck, + self.num_bootstrap, + self.do_control, + self.control_marker, + self.manhattan_plot, + self.first_run, + self.output_files) else: results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.run_original_reaper(self.this_trait, self.dataset, @@ -371,7 +371,7 @@ class RunMapping: ps=this_ps, url="/show_trait?trait_id=" + \ marker['name'] + "&dataset=" + \ - self.dataset.group.name + "Geno" + self.dataset.group.name + "Geno" ) if self.geno_db_exists == "True": @@ -382,7 +382,7 @@ class RunMapping: pos=this_ps, url="/show_trait?trait_id=" + \ marker['name'] + "&dataset=" + \ - self.dataset.group.name + "Geno" + self.dataset.group.name + "Geno" ) else: annot_marker = dict( @@ -409,11 +409,11 @@ class RunMapping: if 'Mb' in marker.keys(): marker['display_pos'] = "Chr" + \ str(marker['chr']) + ": " + \ - "{:.6f}".format(marker['Mb']) + "{:.6f}".format(marker['Mb']) elif 'cM' in marker.keys(): marker['display_pos'] = "Chr" + \ str(marker['chr']) + ": " + \ - "{:.3f}".format(marker['cM']) + "{:.3f}".format(marker['cM']) else: marker['display_pos'] = "N/A" self.qtl_results.append(marker) @@ -776,7 +776,7 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples): perm_strata_strings.append(combined_string) d = dict([(y, x + 1) - for x, y in enumerate(sorted(set(perm_strata_strings)))]) + for x, y in enumerate(sorted(set(perm_strata_strings)))]) list_to_numbers = [d[x] for x in perm_strata_strings] perm_strata = list_to_numbers diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py index 55b0278a..822900cc 100644 --- a/wqflask/wqflask/model.py +++ b/wqflask/wqflask/model.py @@ -45,8 +45,8 @@ class User(Base): ) user_collections = relationship("UserCollection", - order_by="asc(UserCollection.name)", - lazy='dynamic', + order_by="asc(UserCollection.name)", + lazy='dynamic', ) def display_num_collections(self): diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py index 6b836e20..bd1c4407 100644 --- a/wqflask/wqflask/parser.py +++ b/wqflask/wqflask/parser.py @@ -34,7 +34,7 @@ def parse(pstring): (\w+\s*[=:\>\<][\w\*]+) | # wiki=bar, GO:foobar, etc (".*?") | ('.*?') | # terms in quotes, i.e. "brain weight" ([\w\*\?]+)) # shh, brain, etc """, pstring, - flags=re.VERBOSE) + flags=re.VERBOSE) pstring = [item.strip() for item in pstring if item and item.strip()] diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 2e1cb992..fc48959e 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -173,10 +173,10 @@ class SearchResultPage: if self.dataset.type == "ProbeSet": self.header_data_names = ['index', 'display_name', 'symbol', 'description', - 'location', 'mean', 'lrs_score', 'lrs_location', 'additive'] + 'location', 'mean', 'lrs_score', 'lrs_location', 'additive'] elif self.dataset.type == "Publish": self.header_data_names = ['index', 'display_name', 'description', 'mean', - 'authors', 'pubmed_text', 'lrs_score', 'lrs_location', 'additive'] + 'authors', 'pubmed_text', 'lrs_score', 'lrs_location', 'additive'] elif self.dataset.type == "Geno": self.header_data_names = ['index', 'display_name', 'location'] @@ -273,9 +273,9 @@ class SearchResultPage: if search_ob: search_class = getattr(do_search, search_ob) the_search = search_class(search_term, - search_operator, - self.dataset, - search_type['key'] + search_operator, + self.dataset, + search_type['key'] ) return the_search else: diff --git a/wqflask/wqflask/server_side.py b/wqflask/wqflask/server_side.py index 8ca3a9eb..7f68efad 100644 --- a/wqflask/wqflask/server_side.py +++ b/wqflask/wqflask/server_side.py @@ -49,8 +49,8 @@ class ServerSideTable: column_name = self.header_data_names[column_number - 1] sort_direction = self.request_values['sSortDir_' + str(i)] self.table_rows = sorted(self.table_rows, - key=lambda x: x[column_name], - reverse=is_reverse(sort_direction)) + key=lambda x: x[column_name], + reverse=is_reverse(sort_direction)) def paginate_rows(self): """ diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 3a63c84e..f9d30dba 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -75,7 +75,7 @@ class SampleList: if self.dataset.group.species == "mouse": if len(sample.extra_attributes['rrid'].split(":")) > 1: the_rrid = sample.extra_attributes['rrid'].split(":")[ - 1] + 1] sample.extra_attributes['rrid'] = [ sample.extra_attributes['rrid']] sample.extra_attributes['rrid'].append( @@ -83,7 +83,7 @@ class SampleList: elif self.dataset.group.species == "rat": if len(str(sample.extra_attributes['rrid'])): the_rrid = sample.extra_attributes['rrid'].split("_")[ - 1] + 1] sample.extra_attributes['rrid'] = [ sample.extra_attributes['rrid']] sample.extra_attributes['rrid'].append( diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py index 81e7903b..7fabc3f6 100644 --- a/wqflask/wqflask/show_trait/export_trait_data.py +++ b/wqflask/wqflask/show_trait/export_trait_data.py @@ -41,7 +41,7 @@ def get_export_metadata(trait_id, dataset_name): if dataset.type == "Publish": metadata.append(["Phenotype ID: " + trait_id]) metadata.append(["Phenotype URL: " + "http://genenetwork.org/show_trait?trait_id=" + \ - trait_id + "&dataset=" + dataset_name]) + trait_id + "&dataset=" + dataset_name]) metadata.append(["Group: " + dataset.group.name]) metadata.append( ["Phenotype: " + this_trait.description_display.replace(",", "\",\"")]) @@ -56,7 +56,7 @@ def get_export_metadata(trait_id, dataset_name): else: metadata.append(["Record ID: " + trait_id]) metadata.append(["Trait URL: " + "http://genenetwork.org/show_trait?trait_id=" + \ - trait_id + "&dataset=" + dataset_name]) + trait_id + "&dataset=" + dataset_name]) if this_trait.symbol: metadata.append(["Symbol: " + this_trait.symbol]) metadata.append(["Dataset: " + dataset.name]) diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py index 5b7a663c..42fe339e 100644 --- a/wqflask/wqflask/snp_browser/snp_browser.py +++ b/wqflask/wqflask/snp_browser/snp_browser.py @@ -294,7 +294,7 @@ class SnpBrowser: effect_info_dict = get_effect_info(effect_list) coding_domain_list = ['Start Gained', 'Start Lost', - 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] + 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] intron_domain_list = ['Splice Site', 'Nonsplice Site'] for key in effect_info_dict: @@ -320,7 +320,7 @@ class SnpBrowser: if self.redundant == "false" or last_mb != mb: # filter redundant if self.include_record(domain, function, snp_source, conservation_score): info_list = [snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, - function, function_details, snp_source, conservation_score, snp_id] + function, function_details, snp_source, conservation_score, snp_id] info_list.extend(self.allele_list) filtered_results.append(info_list) last_mb = mb @@ -351,7 +351,7 @@ class SnpBrowser: if self.redundant == "false" or last_mb != mb: if self.include_record(domain, function, snp_source, conservation_score): info_list = [snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, - function, function_details, snp_source, conservation_score, snp_id] + function, function_details, snp_source, conservation_score, snp_id] info_list.extend(self.allele_list) filtered_results.append(info_list) last_mb = mb @@ -366,7 +366,7 @@ class SnpBrowser: domain = conservation_score = snp_id = snp_name = rs = flank_3 = flank_5 = ncbi = function = "" if self.include_record(domain, function, source_name, conservation_score): filtered_results.append([indel_name, indel_chr, indel_mb_start, indel_mb_end, - indel_strand, indel_type, indel_size, indel_sequence, source_name]) + indel_strand, indel_type, indel_size, indel_sequence, source_name]) last_mb = indel_mb_start else: @@ -703,9 +703,9 @@ def get_header_list(variant_type, strains, species=None, empty_columns=None): header_data_names = [] if variant_type == "SNP": header_fields.append(['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'Source', 'ConScore', - 'Gene', 'Transcript', 'Exon', 'Domain 1', 'Domain 2', 'Function', 'Details']) + 'Gene', 'Transcript', 'Exon', 'Domain 1', 'Domain 2', 'Function', 'Details']) header_data_names = ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles', 'snp_source', 'conservation_score', - 'gene_name', 'transcript', 'exon', 'domain_1', 'domain_2', 'function', 'function_details'] + 'gene_name', 'transcript', 'exon', 'domain_1', 'domain_2', 'function', 'function_details'] header_fields.append(strain_list) header_data_names += strain_list @@ -742,9 +742,9 @@ def get_header_list(variant_type, strains, species=None, empty_columns=None): elif variant_type == "InDel": header_fields = ['Index', 'ID', 'Type', 'InDel Chr', - 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'] + 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'] header_data_names = ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s', - 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'] + 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'] return header_fields, empty_field_count, header_data_names @@ -758,9 +758,9 @@ def get_effect_details_by_category(effect_name=None, effect_value=None): tmp_list = [] gene_group_list = ['Upstream', 'Downstream', - 'Splice Site', 'Nonsplice Site', '3\' UTR'] + 'Splice Site', 'Nonsplice Site', '3\' UTR'] biotype_group_list = ['Unknown Effect In Exon', 'Start Gained', - 'Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] + 'Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] new_codon_group_list = ['Start Gained'] codon_effect_group_list = [ 'Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] @@ -913,7 +913,7 @@ def get_gene_id_name_dict(species_id, gene_name_list): if len(gene_name_list) == 0: return "" gene_name_str_list = ["'" + gene_name + \ - "'" for gene_name in gene_name_list] + "'" for gene_name in gene_name_list] gene_name_str = ",".join(gene_name_str_list) query = """ diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py index 725e7c9e..0d5f1f3e 100644 --- a/wqflask/wqflask/user_login.py +++ b/wqflask/wqflask/user_login.py @@ -59,12 +59,12 @@ def encode_password(pass_gen_fields, unencrypted_password): def set_password(password): pass_gen_fields = { - "unencrypted_password": password, - "algorithm": "pbkdf2", - "hashfunc": "sha256", - "salt": base64.b64encode(os.urandom(32)), - "iterations": 100000, - "keylength": 32, + "unencrypted_password": password, + "algorithm": "pbkdf2", + "hashfunc": "sha256", + "salt": base64.b64encode(os.urandom(32)), + "iterations": 100000, + "keylength": 32, "created_timestamp": timestamp() } @@ -89,18 +89,18 @@ def get_signed_session_id(user): if 'github_id' in user: session = dict(login_time=time.time(), - user_type="github", - user_id=user['user_id'], - github_id=user['github_id'], - user_name=user['name'], - user_url=user['user_url']) + user_type="github", + user_id=user['user_id'], + github_id=user['github_id'], + user_name=user['name'], + user_url=user['user_url']) elif 'orcid' in user: session = dict(login_time=time.time(), - user_type="orcid", - user_id=user['user_id'], - github_id=user['orcid'], - user_name=user['name'], - user_url=user['user_url']) + user_type="orcid", + user_id=user['user_id'], + github_id=user['orcid'], + user_name=user['name'], + user_url=user['user_url']) else: session = dict(login_time=time.time(), user_type="gn2", @@ -269,7 +269,7 @@ def github_oauth2(): result = requests.post( "https://github.com/login/oauth/access_token", json=data) result_dict = {arr[0]: arr[1] - for arr in [tok.split("=") for tok in result.text.split("&")]} + for arr in [tok.split("=") for tok in result.text.split("&")]} github_user = get_github_user_details(result_dict["access_token"]) diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index 9ebec405..fb26bfb1 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -475,7 +475,7 @@ def set_password(password, user): pwfields.encrypt_time = enc_password.encrypt_time user.password = json.dumps(pwfields.__dict__, - sort_keys=True, + sort_keys=True, ) diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py index 3e543445..67e2e158 100644 --- a/wqflask/wqflask/user_session.py +++ b/wqflask/wqflask/user_session.py @@ -105,8 +105,8 @@ class UserSession: if user_cookie: self.logged_in = False self.record = dict(login_time=time.time(), - user_type="anon", - user_id=str(uuid.uuid4())) + user_type="anon", + user_id=str(uuid.uuid4())) Redis.hmset(self.redis_key, self.record) Redis.expire(self.redis_key, THIRTY_DAYS) @@ -117,8 +117,8 @@ class UserSession: return None else: self.record = dict(login_time=time.time(), - user_type="anon", - user_id=str(uuid.uuid4())) + user_type="anon", + user_id=str(uuid.uuid4())) Redis.hmset(self.redis_key, self.record) Redis.expire(self.redis_key, THIRTY_DAYS) else: diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py index 21516b30..f96892a0 100644 --- a/wqflask/wqflask/wgcna/wgcna_analysis.py +++ b/wqflask/wqflask/wgcna/wgcna_analysis.py @@ -70,7 +70,7 @@ class WGCNA: self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')] print(("Retrieved phenotype data from database", - requestform['trait_list'])) + requestform['trait_list'])) helper_functions.get_trait_db_obs(self, self.trait_db_list) # self.input contains the phenotype values we need to send to R |