Removed list

1 files changed, 0 insertions, 610 deletions

diff --git a/unused.txt b/unused.txt
deleted file mode 100644
index 8eab64ea..00000000
--- a/unused.txt
+++ /dev/null
@@ -1,610 +0,0 @@
-wqflask/base/data_set.py:32: unused import 'itemgetter' (90% confidence)
-wqflask/base/data_set.py:271: unused attribute 'genetic_type' (60% confidence)
-wqflask/base/data_set.py:273: unused attribute 'genetic_type' (60% confidence)
-wqflask/base/data_set.py:281: unused attribute 'accession_id' (60% confidence)
-wqflask/base/data_set.py:282: unused attribute 'mapping_id' (60% confidence)
-wqflask/base/data_set.py:282: unused attribute 'mapping_names' (60% confidence)
-wqflask/base/data_set.py:319: unused function 'get_specified_markers' (60% confidence)
-wqflask/base/data_set.py:460: unused variable 'dataset_sub_menu' (60% confidence)
-wqflask/base/data_set.py:463: unused variable 'tissue_position' (60% confidence)
-wqflask/base/data_set.py:467: unused variable 'tissue_position' (60% confidence)
-wqflask/base/data_set.py:660: unused class 'PhenotypeDataSet' (60% confidence)
-wqflask/base/data_set.py:722: unused function 'get_trait_list' (60% confidence)
-wqflask/base/data_set.py:751: unreachable code after 'continue' (100% confidence)
-wqflask/base/data_set.py:773: unused attribute 'LRS_score_value' (60% confidence)
-wqflask/base/data_set.py:775: unused attribute 'LRS_location_value' (60% confidence)
-wqflask/base/data_set.py:794: unused variable 'LRS_location_value' (60% confidence)
-wqflask/base/data_set.py:797: unused variable 'LRS_location_value' (60% confidence)
-wqflask/base/data_set.py:799: unused variable 'LRS_location_value' (60% confidence)
-wqflask/base/data_set.py:802: unused attribute 'LRS_score_value' (60% confidence)
-wqflask/base/data_set.py:802: unused variable 'LRS_score_value' (60% confidence)
-wqflask/base/data_set.py:828: unused class 'GenotypeDataSet' (60% confidence)
-wqflask/base/data_set.py:864: unused function 'get_trait_list' (60% confidence)
-wqflask/base/data_set.py:884: unused variable 'trait_location_repr' (60% confidence)
-wqflask/base/data_set.py:897: unused attribute 'location_value' (60% confidence)
-wqflask/base/data_set.py:923: unused class 'MrnaAssayDataSet' (60% confidence)
-wqflask/base/data_set.py:992: unused function 'get_trait_list_1' (60% confidence)
-wqflask/base/data_set.py:1038: unused variable 'trait_location_repr' (60% confidence)
-wqflask/base/data_set.py:1057: unused attribute 'location_value' (60% confidence)
-wqflask/base/data_set.py:1079: unused attribute 'LRS_score_value' (60% confidence)
-wqflask/base/data_set.py:1081: unused attribute 'LRS_location_value' (60% confidence)
-wqflask/base/data_set.py:1097: unused variable 'lrs_location_value' (60% confidence)
-wqflask/base/data_set.py:1099: unused attribute 'LRS_score_value' (60% confidence)
-wqflask/base/data_set.py:1115: unused function 'get_sequence' (60% confidence)
-wqflask/base/data_set.py:1167: unused class 'TempDataSet' (60% confidence)
-wqflask/base/data_set.py:1207: unused function 'get_group' (60% confidence)
-wqflask/base/data_set.py:1218: unused attribute 'group_id' (60% confidence)
-wqflask/base/mrna_assay_tissue_data.py:21: unused attribute 'have_data' (60% confidence)
-wqflask/base/species.py:21: unused attribute 'genome_mb_length' (60% confidence)
-wqflask/base/species.py:45: unused function 'set_cm_length' (60% confidence)
-wqflask/base/species.py:77: unused attribute 'mb_graph_interval' (60% confidence)
-wqflask/base/species.py:79: unused attribute 'mb_graph_interval' (60% confidence)
-wqflask/base/species.py:94: unused function 'get_genome_cm_length' (60% confidence)
-wqflask/base/species.py:99: unused function 'get_cm_length_list' (60% confidence)
-wqflask/base/template.py:27: unused variable 'template' (60% confidence)
-wqflask/base/trait.py:28: unused function 'print_mem' (60% confidence)
-wqflask/base/trait.py:58: unused attribute 'pvalue' (60% confidence)
-wqflask/base/trait.py:66: unused attribute 'LRS_score_value' (60% confidence)
-wqflask/base/trait.py:68: unused attribute 'LRS_location_value' (60% confidence)
-wqflask/base/trait.py:86: unused function 'get_name' (60% confidence)
-wqflask/base/trait.py:97: unused function 'get_given_name' (60% confidence)
-wqflask/base/trait.py:118: unused function 'display_name' (60% confidence)
-wqflask/base/trait.py:148: unused function 'export_data' (60% confidence)
-wqflask/base/trait.py:189: unused property 'name_header_fmt' (60% confidence)
-wqflask/base/trait.py:201: unused property 'description_fmt' (60% confidence)
-wqflask/base/trait.py:220: unused property 'alias_fmt' (60% confidence)
-wqflask/base/trait.py:232: unused property 'location_fmt' (60% confidence)
-wqflask/base/trait.py:261: unused function 'getSequence' (60% confidence)
-wqflask/base/trait.py:309: unused function 'get_sample_data' (60% confidence)
-wqflask/base/trait.py:546: unused attribute 'homologeneid' (60% confidence)
-wqflask/base/trait.py:575: unused attribute 'homologeneid' (60% confidence)
-wqflask/base/trait.py:594: unused attribute 'location_value' (60% confidence)
-wqflask/base/trait.py:611: unused attribute 'location_value' (60% confidence)
-wqflask/base/trait.py:615: unused attribute 'location_value' (60% confidence)
-wqflask/base/trait.py:624: unused attribute 'location_value' (60% confidence)
-wqflask/base/trait.py:629: unused attribute 'LRS_score_value' (60% confidence)
-wqflask/base/trait.py:631: unused attribute 'LRS_location_value' (60% confidence)
-wqflask/base/trait.py:646: unused attribute 'pvalue' (60% confidence)
-wqflask/base/trait.py:664: unused attribute 'pvalue' (60% confidence)
-wqflask/base/trait.py:704: unused variable 'LRS_location_value' (60% confidence)
-wqflask/base/trait.py:707: unused variable 'LRS_location_value' (60% confidence)
-wqflask/base/trait.py:709: unused variable 'LRS_location_value' (60% confidence)
-wqflask/base/trait.py:714: unused attribute 'LRS_score_value' (60% confidence)
-wqflask/base/trait.py:714: unused variable 'LRS_score_value' (60% confidence)
-wqflask/base/webqtlCaseData.py:42: unused attribute 'this_id' (60% confidence)
-wqflask/base/webqtlCaseData.py:59: unused property 'class_outlier' (60% confidence)
-wqflask/base/webqtlCaseData.py:67: unused property 'display_value' (60% confidence)
-wqflask/base/webqtlCaseData.py:74: unused property 'display_variance' (60% confidence)
-wqflask/base/webqtlConfig.py:24: unused variable 'MULTIPLEMAPPINGLIMIT' (60% confidence)
-wqflask/base/webqtlConfig.py:27: unused variable 'MAXCORR' (60% confidence)
-wqflask/base/webqtlConfig.py:36: unused variable 'MAXLIFE' (60% confidence)
-wqflask/base/webqtlConfig.py:42: unused variable 'NCBI_LOCUSID' (60% confidence)
-wqflask/base/webqtlConfig.py:43: unused variable 'UCSC_REFSEQ' (60% confidence)
-wqflask/base/webqtlConfig.py:44: unused variable 'GENBANK_ID' (60% confidence)
-wqflask/base/webqtlConfig.py:45: unused variable 'OMIM_ID' (60% confidence)
-wqflask/base/webqtlConfig.py:46: unused variable 'UNIGEN_ID' (60% confidence)
-wqflask/base/webqtlConfig.py:47: unused variable 'HOMOLOGENE_ID' (60% confidence)
-wqflask/base/webqtlConfig.py:49: unused variable 'UCSC_POS' (60% confidence)
-wqflask/base/webqtlConfig.py:53: unused variable 'UCSC_GENOME' (60% confidence)
-wqflask/base/webqtlConfig.py:54: unused variable 'ENSEMBLE_BLAT' (60% confidence)
-wqflask/base/webqtlConfig.py:55: unused variable 'DBSNP' (60% confidence)
-wqflask/base/webqtlConfig.py:56: unused variable 'UCSC_RUDI_TRACK_URL' (60% confidence)
-wqflask/base/webqtlConfig.py:57: unused variable 'GENOMEBROWSER_URL' (60% confidence)
-wqflask/base/webqtlConfig.py:58: unused variable 'ENSEMBLETRANSCRIPT_URL' (60% confidence)
-wqflask/base/webqtlFormData.py:53: unused variable 'mod_python_session' (60% confidence)
-wqflask/base/webqtlFormData.py:54: unused variable 'FieldStorage_formdata' (60% confidence)
-wqflask/base/webqtlFormData.py:61: unused attribute 'varianceDispName' (60% confidence)
-wqflask/base/webqtlFormData.py:74: unused attribute 'refURL' (60% confidence)
-wqflask/base/webqtlFormData.py:76: unused attribute 'refURL' (60% confidence)
-wqflask/base/webqtlFormData.py:328: unused function 'Sample' (60% confidence)
-wqflask/basicStatistics/BasicStatisticsFunctions.py:21: unused function 'basicStatsTable' (60% confidence)
-wqflask/basicStatistics/BasicStatisticsFunctions.py:101: unused function 'plotNormalProbability' (60% confidence)
-wqflask/basicStatistics/BasicStatisticsFunctions.py:155: unused function 'plotBarGraph' (60% confidence)
-wqflask/basicStatistics/corestats.py:61: unused function 'median' (60% confidence)
-wqflask/maintenance/convert_geno_to_bimbam.py:74: unused attribute 'geno_fh' (60% confidence)
-wqflask/maintenance/convert_geno_to_bimbam.py:82: unused variable 'row_count' (60% confidence)
-wqflask/maintenance/gen_select_dataset.py:69: unused variable 'db_uri' (60% confidence)
-wqflask/maintenance/gen_select_dataset.py:302: unused function '_test_it' (60% confidence)
-wqflask/maintenance/get_group_samplelists.py:9: unused function 'process_genofiles' (60% confidence)
-wqflask/mock/es_double.py:1: unused class 'ESDouble' (60% confidence)
-wqflask/run_gunicorn.py:17: unused function 'hello' (60% confidence)
-wqflask/utility/after.py:18: unused function 'call_after_request_callbacks' (60% confidence)
-wqflask/utility/AJAX_table.py:41: unused class 'AJAX_table' (60% confidence)
-wqflask/utility/benchmark.py:6: unused import 'LOG_BENCH' (90% confidence)
-wqflask/utility/elasticsearch_tools.py:51: unused variable 'te' (60% confidence)
-wqflask/utility/genofile_parser.py:75: unused variable 'row_count' (60% confidence)
-wqflask/utility/logger.py:36: unused import 'LOG_FORMAT' (90% confidence)
-wqflask/utility/logger.py:59: unused function 'debug20' (60% confidence)
-wqflask/utility/logger.py:84: unused function 'infof' (60% confidence)
-wqflask/utility/Plot.py:167: unused function 'erf' (60% confidence)
-wqflask/utility/Plot.py:182: unused function 'calMeanVar' (60% confidence)
-wqflask/utility/Plot.py:370: unused variable 'tstrain' (60% confidence)
-wqflask/utility/Plot.py:449: unused function 'plotSecurity' (60% confidence)
-wqflask/utility/Plot.py:594: unused variable 'Xll' (60% confidence)
-wqflask/utility/Plot.py:595: unused variable 'Xur' (60% confidence)
-wqflask/utility/Plot.py:914: unused function 'plotXYSVG' (60% confidence)
-wqflask/utility/Plot.py:914: unused variable 'plotColor' (60% confidence)
-wqflask/utility/Plot.py:923: unused variable 'dataXAlt' (60% confidence)
-wqflask/utility/Plot.py:924: unused variable 'dataYAlt' (60% confidence)
-wqflask/utility/Plot.py:929: unused variable 'dataXAlt' (60% confidence)
-wqflask/utility/Plot.py:930: unused variable 'dataYAlt' (60% confidence)
-wqflask/utility/Plot.py:1030: unused attribute 'argv' (60% confidence)
-wqflask/utility/Plot.py:1117: unused variable 'bufferSpace' (60% confidence)
-wqflask/utility/Plot.py:1156: unused function 'colorSpectrumOld' (60% confidence)
-wqflask/utility/Plot.py:1234: unused function 'colorSpectrumSVG' (60% confidence)
-wqflask/utility/Plot.py:1257: unused function 'BWSpectrum' (60% confidence)
-wqflask/utility/svg.py:116: unused attribute 'setrecursionlimit' (60% confidence)
-wqflask/utility/svg.py:174: unused function '_pointlist' (60% confidence)
-wqflask/utility/svg.py:186: unused function 'closepath' (60% confidence)
-wqflask/utility/svg.py:189: unused function 'move' (60% confidence)
-wqflask/utility/svg.py:192: unused function 'relmove' (60% confidence)
-wqflask/utility/svg.py:198: unused function 'relline' (60% confidence)
-wqflask/utility/svg.py:201: unused function 'hline' (60% confidence)
-wqflask/utility/svg.py:204: unused function 'relhline' (60% confidence)
-wqflask/utility/svg.py:207: unused function 'vline' (60% confidence)
-wqflask/utility/svg.py:210: unused function 'relvline' (60% confidence)
-wqflask/utility/svg.py:213: unused function 'bezier' (60% confidence)
-wqflask/utility/svg.py:216: unused function 'relbezier' (60% confidence)
-wqflask/utility/svg.py:219: unused function 'smbezier' (60% confidence)
-wqflask/utility/svg.py:225: unused function 'qbezier' (60% confidence)
-wqflask/utility/svg.py:228: unused function 'relqbezier' (60% confidence)
-wqflask/utility/svg.py:231: unused function 'smqbezier' (60% confidence)
-wqflask/utility/svg.py:234: unused function 'relsmqbezier' (60% confidence)
-wqflask/utility/svg.py:237: unused function 'ellarc' (60% confidence)
-wqflask/utility/svg.py:240: unused function 'relellarc' (60% confidence)
-wqflask/utility/svg.py:359: unused class 'spannedtext' (60% confidence)
-wqflask/utility/svg.py:382: unused function 'addtext' (60% confidence)
-wqflask/utility/svg.py:384: unused function 'addtspan' (60% confidence)
-wqflask/utility/svg.py:386: unused function 'addtref' (60% confidence)
-wqflask/utility/svg.py:494: unused class 'polyline' (60% confidence)
-wqflask/utility/svg.py:508: unused class 'polygon' (60% confidence)
-wqflask/utility/svg.py:560: unused class 'textpath' (60% confidence)
-wqflask/utility/svg.py:612: unused class 'lineargradient' (60% confidence)
-wqflask/utility/svg.py:631: unused class 'radialgradient' (60% confidence)
-wqflask/utility/svg.py:652: unused class 'stop' (60% confidence)
-wqflask/utility/svg.py:662: unused class 'style' (60% confidence)
-wqflask/utility/svg.py:671: unused class 'image' (60% confidence)
-wqflask/utility/svg.py:747: unused class 'defs' (60% confidence)
-wqflask/utility/svg.py:755: unused class 'switch' (60% confidence)
-wqflask/utility/svg.py:793: unused class 'view' (60% confidence)
-wqflask/utility/svg.py:802: unused class 'script' (60% confidence)
-wqflask/utility/svg.py:811: unused class 'animate' (60% confidence)
-wqflask/utility/svg.py:837: unused class 'animateTransform' (60% confidence)
-wqflask/utility/svg.py:853: unused class 'animateColor' (60% confidence)
-wqflask/utility/svg.py:1022: unused function 'validate' (60% confidence)
-wqflask/utility/temp_data.py:13: unused function 'store' (60% confidence)
-wqflask/utility/tools.py:182: unused function 'locate_phewas' (60% confidence)
-wqflask/utility/tools.py:235: unused variable 'HOME' (60% confidence)
-wqflask/utility/tools.py:243: unused variable 'LOG_BENCH' (60% confidence)
-wqflask/utility/tools.py:244: unused variable 'LOG_FORMAT' (60% confidence)
-wqflask/utility/tools.py:248: unused variable 'GENENETWORK_FILES' (60% confidence)
-wqflask/utility/tools.py:251: unused variable 'JS_GN_PATH' (60% confidence)
-wqflask/utility/webqtlUtil.py:69: unused variable 'IMGSTEP1' (60% confidence)
-wqflask/utility/webqtlUtil.py:70: unused variable 'IMGSTEP2' (60% confidence)
-wqflask/utility/webqtlUtil.py:71: unused variable 'IMGSTEP3' (60% confidence)
-wqflask/utility/webqtlUtil.py:72: unused variable 'IMGNEXT' (60% confidence)
-wqflask/utility/webqtlUtil.py:87: unused variable 'PROGRESSBAR' (60% confidence)
-wqflask/utility/webqtlUtil.py:157: unused function 'decodeEscape' (60% confidence)
-wqflask/utility/webqtlUtil.py:203: unused function 'toInt' (60% confidence)
-wqflask/utility/webqtlUtil.py:220: unused function 'transpose' (60% confidence)
-wqflask/utility/webqtlUtil.py:225: unused function 'asymTranspose' (60% confidence)
-wqflask/utility/webqtlUtil.py:241: unused function 'generate_session' (60% confidence)
-wqflask/utility/webqtlUtil.py:245: unused function 'cvt2Dict' (60% confidence)
-wqflask/utility/webqtlUtil.py:251: unused function 'dump_session' (60% confidence)
-wqflask/utility/webqtlUtil.py:276: unused function 'FloatAsFloat' (60% confidence)
-wqflask/utility/webqtlUtil.py:283: unused function 'RemoveZero' (60% confidence)
-wqflask/utility/webqtlUtil.py:306: unused function 'FloatList2String' (60% confidence)
-wqflask/utility/webqtlUtil.py:332: unused function 'FileDataProcess' (60% confidence)
-wqflask/utility/webqtlUtil.py:372: unused function 'cmpScanResult' (60% confidence)
-wqflask/utility/webqtlUtil.py:384: unused function 'cmpScanResult2' (60% confidence)
-wqflask/utility/webqtlUtil.py:596: unused function 'calCorrelationRankText' (60% confidence)
-wqflask/utility/webqtlUtil.py:715: unused function 'calCorrelationText' (60% confidence)
-wqflask/utility/webqtlUtil.py:761: unused function 'cmpCorr' (60% confidence)
-wqflask/utility/webqtlUtil.py:772: unused function 'cmpLitCorr' (60% confidence)
-wqflask/utility/webqtlUtil.py:783: unused function 'cmpPValue' (60% confidence)
-wqflask/utility/webqtlUtil.py:811: unused function 'cmpLRSFull' (60% confidence)
-wqflask/utility/webqtlUtil.py:822: unused function 'cmpLRSInteract' (60% confidence)
-wqflask/utility/webqtlUtil.py:834: unused function 'cmpPos' (60% confidence)
-wqflask/utility/webqtlUtil.py:858: unused function 'cmpGenoPos' (60% confidence)
-wqflask/utility/webqtlUtil.py:895: unused class 'VisualizeException' (60% confidence)
-wqflask/utility/webqtlUtil.py:912: unused function 'safeFloat' (60% confidence)
-wqflask/utility/webqtlUtil.py:917: unused function 'safeInt' (60% confidence)
-wqflask/utility/webqtlUtil.py:923: unused function 'safeString' (60% confidence)
-wqflask/utility/webqtlUtil.py:931: unused function 'yesNoToInt' (60% confidence)
-wqflask/utility/webqtlUtil.py:941: unused function 'intToYesNo' (60% confidence)
-wqflask/utility/webqtlUtil.py:949: unused function 'formatField' (60% confidence)
-wqflask/utility/webqtlUtil.py:971: unused variable 'last_idx' (60% confidence)
-wqflask/utility/webqtlUtil.py:981: unused variable 'last_idx' (60% confidence)
-wqflask/wqflask/__init__.py:24: unused import 'wqflask' (90% confidence)
-wqflask/wqflask/collect.py:43: unused function 'get_collection' (60% confidence)
-wqflask/wqflask/collect.py:225: unused function 'collections_add' (60% confidence)
-wqflask/wqflask/collect.py:247: unused function 'collections_new' (60% confidence)
-wqflask/wqflask/collect.py:285: unused variable 'current_collections' (60% confidence)
-wqflask/wqflask/collect.py:291: unused function 'list_collections' (60% confidence)
-wqflask/wqflask/collect.py:368: unused function 'view_collection' (60% confidence)
-wqflask/wqflask/correlation/corr_scatter_plot.py:22: unused attribute 'width' (60% confidence)
-wqflask/wqflask/correlation/corr_scatter_plot.py:28: unused attribute 'height' (60% confidence)
-wqflask/wqflask/correlation/corr_scatter_plot.py:34: unused attribute 'circle_color' (60% confidence)
-wqflask/wqflask/correlation/corr_scatter_plot.py:40: unused attribute 'circle_radius' (60% confidence)
-wqflask/wqflask/correlation/corr_scatter_plot.py:46: unused attribute 'line_color' (60% confidence)
-wqflask/wqflask/correlation/corr_scatter_plot.py:52: unused attribute 'line_width' (60% confidence)
-wqflask/wqflask/correlation/corr_scatter_plot.py:69: unused variable 'std_err' (60% confidence)
-wqflask/wqflask/correlation/corr_scatter_plot.py:76: unused variable 'srstd_err' (60% confidence)
-wqflask/wqflask/correlation/corr_scatter_plot.py:107: unused attribute 'jsdata' (60% confidence)
-wqflask/wqflask/correlation/correlation_functions.py:45: unused function 'controlStrains' (60% confidence)
-wqflask/wqflask/correlation/correlation_functions.py:81: unused function 'fixStrains' (60% confidence)
-wqflask/wqflask/correlation/correlation_functions.py:124: unused function 'findIdenticalControlTraits' (60% confidence)
-wqflask/wqflask/correlation/correlation_functions.py:150: unused function 'findIdenticalTraits' (60% confidence)
-wqflask/wqflask/correlation/correlation_functions.py:185: unused function 'determinePartialsByR' (60% confidence)
-wqflask/wqflask/correlation/correlation_functions.py:497: unused function 'calZeroOrderCorr' (60% confidence)
-wqflask/wqflask/correlation/correlation_functions.py:502: unused variable 'primary_var' (60% confidence)
-wqflask/wqflask/correlation/correlation_functions.py:681: unused function 'getTissueProbeSetXRefInfo' (60% confidence)
-wqflask/wqflask/correlation/correlation_functions.py:727: unused variable 'resultCount' (60% confidence)
-wqflask/wqflask/correlation/correlation_functions.py:759: unused function 'get_symbol_value_pairs' (60% confidence)
-wqflask/wqflask/correlation/correlation_functions.py:881: unused function 'getCorrPvArray' (60% confidence)
-wqflask/wqflask/correlation/correlation_functions.py:941: unused function 'calculateCorrOfAllTissueTrait' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:26: unused import 'gc' (90% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:67: unused variable 'METHOD_SAMPLE_PEARSON' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:68: unused variable 'METHOD_SAMPLE_RANK' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:77: unused function 'print_mem' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:81: unused class 'AuthException' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:86: unused variable 'corr_min_informative' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:178: unused variable 'cache_available' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:264: unused attribute 'tissue_pvalue' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:268: unused attribute 'tissue_pvalue' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:282: unused attribute 'tissue_pvalue' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:286: unused attribute 'tissue_pvalue' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:301: unused attribute 'json_results' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:356: unused attribute 'formatted_corr_type' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:358: unused attribute 'formatted_corr_type' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:360: unused attribute 'formatted_corr_type' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:362: unused attribute 'formatted_corr_type' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:365: unused attribute 'formatted_corr_type' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:367: unused attribute 'formatted_corr_type' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:399: unused attribute 'tissue_pvalue' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:685: unused function 'do_tissue_corr_for_all_traits_2' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:739: unused variable 'tissue_probesetfreeze_id' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:784: unused variable 'primary_trait_value' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:786: unused variable 'symbol_value_dict' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:836: unused variable 'tissueProbeSetFreezeId' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:930: unused attribute 'p_tissue' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:975: unused variable 'mouse_geneid1' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:1033: unused function 'get_traits' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:1036: unsatisfiable 'if' condition (100% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:1039: unused variable 'use_lit' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:1042: unused variable 'use_lit' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:1044: unused variable 'use_tissue_corr' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:1047: unused variable 'use_tissue_corr' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:1081: unused attribute 'p_tissue' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:1095: unused variable 'totalTraits' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:1107: unused variable 'primary_trait_value' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:1109: unused variable 'symbol_value_dict' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:1125: unused function 'correlate' (60% confidence)
-wqflask/wqflask/correlation/show_corr_results.py:1152: unused function 'do_parallel_correlation' (60% confidence)
-wqflask/wqflask/correlation_matrix/show_corr_matrix.py:26: unused import 'gc' (90% confidence)
-wqflask/wqflask/correlation_matrix/show_corr_matrix.py:177: unused attribute 'pca_works' (60% confidence)
-wqflask/wqflask/correlation_matrix/show_corr_matrix.py:179: unused attribute 'loadings_array' (60% confidence)
-wqflask/wqflask/correlation_matrix/show_corr_matrix.py:181: unused attribute 'pca_works' (60% confidence)
-wqflask/wqflask/correlation_matrix/show_corr_matrix.py:218: unused attribute 'scores' (60% confidence)
-wqflask/wqflask/correlation_matrix/show_corr_matrix.py:219: unused attribute 'scale' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:5: unused import 'sp' (90% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:27: unused variable 'utils' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:32: unused variable 'r_read_csv' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:33: unused variable 'r_dim' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:37: unused variable 'r_paste' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:39: unused variable 'r_head' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:44: unused variable 'r_matrix' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:45: unused variable 'r_seq' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:47: unused variable 'r_names' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:48: unused variable 'r_sink' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:49: unused variable 'r_is_NA' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:50: unused variable 'r_file' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:53: unused variable 'r_save_image' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:54: unused variable 'r_class' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:55: unused variable 'r_save' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:56: unused variable 'r_write_table' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:57: unused variable 'r_read_table' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:58: unused variable 'r_as_data_frame' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:75: unused attribute 'r_CTLnetwork' (60% confidence)
-wqflask/wqflask/ctl/ctl_analysis.py:76: unused attribute 'r_CTLprofiles' (60% confidence)
-wqflask/wqflask/database.py:26: unused import 'wqflask' (90% confidence)
-wqflask/wqflask/do_search.py:82: unused class 'QuickMrnaAssaySearch' (60% confidence)
-wqflask/wqflask/do_search.py:178: unused function 'run_combined' (60% confidence)
-wqflask/wqflask/do_search.py:286: unused function 'run_combined' (60% confidence)
-wqflask/wqflask/do_search.py:314: unused class 'QuickPhenotypeSearch' (60% confidence)
-wqflask/wqflask/do_search.py:433: unused class 'RifSearch' (60% confidence)
-wqflask/wqflask/do_search.py:456: unused class 'WikiSearch' (60% confidence)
-wqflask/wqflask/do_search.py:481: unused class 'GoSearch' (60% confidence)
-wqflask/wqflask/do_search.py:588: unused class 'MrnaLrsSearch' (60% confidence)
-wqflask/wqflask/do_search.py:601: unused class 'PhenotypeLrsSearch' (60% confidence)
-wqflask/wqflask/do_search.py:685: unused class 'CisLrsSearch' (60% confidence)
-wqflask/wqflask/do_search.py:715: unused class 'TransLrsSearch' (60% confidence)
-wqflask/wqflask/do_search.py:745: unused class 'MeanSearch' (60% confidence)
-wqflask/wqflask/do_search.py:770: unused function 'get_final_query' (60% confidence)
-wqflask/wqflask/do_search.py:786: unused class 'RangeSearch' (60% confidence)
-wqflask/wqflask/do_search.py:861: unused class 'MrnaPositionSearch' (60% confidence)
-wqflask/wqflask/do_search.py:874: unused class 'GenotypePositionSearch' (60% confidence)
-wqflask/wqflask/do_search.py:920: unused class 'AuthorSearch' (60% confidence)
-wqflask/wqflask/docs.py:14: unused attribute 'entry' (60% confidence)
-wqflask/wqflask/docs.py:16: unused attribute 'content' (60% confidence)
-wqflask/wqflask/export_traits.py:3: unused import 'operator' (90% confidence)
-wqflask/wqflask/heatmap/heatmap.py:6: unused import 'gc' (90% confidence)
-wqflask/wqflask/heatmap/heatmap.py:19: unused import 'linalg' (90% confidence)
-wqflask/wqflask/heatmap/heatmap.py:148: unused attribute 'lrs_array' (60% confidence)
-wqflask/wqflask/heatmap/heatmap.py:225: unused function 'gen_pylmm_results' (60% confidence)
-wqflask/wqflask/interval_analyst/GeneUtil.py:9: unused variable 'webqtlDb' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:19: unused import 'linalg' (90% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:84: unused attribute 'geno_db_exists' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:87: unused variable 'geno_dataset' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:88: unused attribute 'geno_db_exists' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:90: unused attribute 'geno_db_exists' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:116: unused attribute 'bootstrap_results' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:120: unused attribute 'selected_chr' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:123: unused attribute 'selected_chr' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:125: unused attribute 'selected_chr' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:135: unused attribute 'haplotypeAnalystCheck' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:143: unused attribute 'LRSCheck' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:146: unused attribute 'showSNP' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:148: unused attribute 'showSNP' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:151: unused attribute 'showGenes' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:153: unused attribute 'showGenes' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:156: unused attribute 'viewLegend' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:158: unused attribute 'viewLegend' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:170: unused attribute 'showSNP' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:171: unused attribute 'showGenes' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:172: unused attribute 'viewLegend' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:203: unused attribute 'additiveCheck' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:205: unused attribute 'additiveCheck' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:213: unused attribute 'additiveCheck' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:228: unused attribute 'bootstrap_results' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:262: unused attribute 'trimmed_markers' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:281: unused attribute 'cutoff' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:293: unused attribute 'trimmed_markers' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:500: unused function 'trim_results' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:565: unused function 'get_lod_score_cutoff' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:600: unused function 'create_snp_iterator_file' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:605: unreachable code after 'raise' (100% confidence)
-wqflask/wqflask/marker_regression/marker_regression.py:655: unused variable 'num_markers' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:33: unused import 'urllib' (90% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:55: unused variable 'maxBootStrap' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:84: unused variable 'MIN_PIXELS_BETWEEN_LABELS' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:96: unused variable 'ALEX_DEBUG_BOOL_COLORIZE_GENES' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:99: unused variable 'kWIDTH_DEFAULT' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:108: unused variable 'GENE_FILL_COLOR' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:109: unused variable 'GENE_OUTLINE_COLOR' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:112: unused variable 'LRS_LINE_WIDTH' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:119: unused variable 'ADDITIVE_COLOR' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:130: unused variable 'QMARK_EDGE_COLOR' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:131: unused variable 'QMARK_FILL_COLOR' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:134: unused variable 'X_AXIS_LABEL_COLOR' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:136: unused variable 'MINI_VIEW_MAGNIFIED_REGION_COLOR' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:137: unused variable 'MINI_VIEW_OUTSIDE_REGION_COLOR' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:138: unused variable 'MINI_VIEW_BORDER_COLOR' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:157: unused variable 'DRAW_UTR_LABELS' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:177: unused attribute 'geno_db_exists' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:185: unused attribute 'mapmethod_rqtl_geno' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:186: unused attribute 'mapmodel_rqtl_geno' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:191: unused attribute 'trimmed_markers' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:311: unused attribute 'cutoff' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:442: unused attribute 'dataSource' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:557: unused variable 'geneTableContainer' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:578: unused attribute 'gifmap' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:587: unused variable 'gifmapX2' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:622: unused attribute 'perm_filename' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:689: unused attribute 'body' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:695: unused function 'writeQTL2Text' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:801: unused variable 'startPixelX' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:802: unused variable 'endPixelX' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1111: unused variable 'locLocation' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1146: unused variable 'locLocation' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1190: unused variable 'lod' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1192: unused variable 'lod' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1208: unused variable 'string3' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1239: unused variable 'displayStartInBases' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1240: unused variable 'displayEndInBases' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1256: unused variable 'geneId' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1310: unused variable 'geneId' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1343: unreachable 'else' block (100% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1347: unused variable 'utrColor' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1453: unused variable 'widthMultiplier' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1457: unused variable 'exprdrawn' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1559: unreachable 'else' block (100% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1691: unused variable 'bandWidth' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1729: unused variable 'traitX' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1737: unused variable 'traitX' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1764: unused variable 'spacingFromLineToLabel' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:1770: unused variable 'graphMbWidth' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2261: unused variable 'maxAdd' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2353: unused function 'calculateAllResult' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2365: unused attribute 'chromosome' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2426: unused attribute 'chromosome' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2459: unused attribute 'chromosome' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2490: unused function 'traitRemapTD' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2609: unused function 'traitInfoTD' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2679: unused function 'permutationTextFile' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2704: unused attribute 'gene_table_header' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2705: unused attribute 'gene_table_body' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2719: unused attribute 'gene_table_header' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2720: unused attribute 'gene_table_body' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2727: unused variable 'gene_tblobj_header' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2731: unused variable 'col_class' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2831: unused variable 'className' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2884: unused variable 'mouseStartValue' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2896: unused variable 'humanChrSort' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2898: unused variable 'humanChrSort' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2900: unused variable 'humanChrSort' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2904: unused variable 'humanStartValue' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2908: unused variable 'humanChrSort' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2908: unused variable 'humanStartValue' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2927: unused variable 'polymiRTS' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2929: unused variable 'polymiRTS' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2938: unused variable 'literatureCorrelation' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:2940: unused variable 'literatureCorrelation' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:3045: unused variable 'humanChrSort' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:3047: unused variable 'humanChrSort' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:3049: unused variable 'humanChrSort' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:3052: unused variable 'humanChrSort' (60% confidence)
-wqflask/wqflask/marker_regression/marker_regression_gn1.py:3110: unused function 'getSortByValue' (60% confidence)
-wqflask/wqflask/marker_regression/MarkerRegressionPage.py:31: unused import 'urllib' (90% confidence)
-wqflask/wqflask/marker_regression/MarkerRegressionPage.py:48: unused class 'MarkerRegressionPage' (60% confidence)
-wqflask/wqflask/marker_regression/MarkerRegressionPage.py:621: unused variable 'startPixelX' (60% confidence)
-wqflask/wqflask/marker_regression/MarkerRegressionPage.py:622: unused variable 'endPixelX' (60% confidence)
-wqflask/wqflask/marker_regression/MarkerRegressionPage.py:667: unused variable 'startPixelX' (60% confidence)
-wqflask/wqflask/marker_regression/MarkerRegressionPage.py:668: unused variable 'endPixelX' (60% confidence)
-wqflask/wqflask/marker_regression/MarkerRegressionPage.py:1001: unused variable 'maxAdd' (60% confidence)
-wqflask/wqflask/marker_regression/MarkerRegressionPage.py:1164: unused variable 'spacingFromLineToLabel' (60% confidence)
-wqflask/wqflask/marker_regression/MarkerRegressionPage.py:1170: unused variable 'graphMbWidth' (60% confidence)
-wqflask/wqflask/marker_regression/MarkerRegressionPage.py:1245: unused variable 'spacingFromLineToLabel' (60% confidence)
-wqflask/wqflask/marker_regression/MarkerRegressionPage.py:1251: unused variable 'graphMbWidth' (60% confidence)
-wqflask/wqflask/marker_regression/plink_mapping.py:111: unused variable 'header_line' (60% confidence)
-wqflask/wqflask/marker_regression/qtlreaper_mapping.py:29: unused variable 'highly_significant' (60% confidence)
-wqflask/wqflask/marker_regression/rqtl_mapping.py:14: unused variable 'r_sum' (60% confidence)
-wqflask/wqflask/marker_regression/rqtl_mapping.py:16: unused variable 'postscript' (60% confidence)
-wqflask/wqflask/marker_regression/rqtl_mapping.py:26: unused variable 'read_cross' (60% confidence)
-wqflask/wqflask/marker_regression/rqtl_mapping.py:27: unused variable 'write_cross' (60% confidence)
-wqflask/wqflask/model.py:9: unused import 'SQLAlchemy' (90% confidence)
-wqflask/wqflask/model.py:15: unused import 'Integer' (90% confidence)
-wqflask/wqflask/model.py:15: unused import 'String' (90% confidence)
-wqflask/wqflask/model.py:15: unused import 'Table' (90% confidence)
-wqflask/wqflask/model.py:17: unused import 'backref' (90% confidence)
-wqflask/wqflask/model.py:45: unused variable 'active' (60% confidence)
-wqflask/wqflask/model.py:47: unused variable 'registration_info' (60% confidence)
-wqflask/wqflask/model.py:65: unused function 'display_num_collections' (60% confidence)
-wqflask/wqflask/model.py:99: unused property 'login_count' (60% confidence)
-wqflask/wqflask/model.py:104: unused property 'confirmed_at' (60% confidence)
-wqflask/wqflask/model.py:112: unused property 'superuser_info' (60% confidence)
-wqflask/wqflask/model.py:119: unused property 'crowner' (60% confidence)
-wqflask/wqflask/model.py:129: unused property 'most_recent_login' (60% confidence)
-wqflask/wqflask/model.py:146: unused variable 'ip_address' (60% confidence)
-wqflask/wqflask/model.py:147: unused variable 'successful' (60% confidence)
-wqflask/wqflask/model.py:155: unused attribute 'ip_address' (60% confidence)
-wqflask/wqflask/model.py:195: unused function 'user_uuid' (60% confidence)
-wqflask/wqflask/model.py:197: unused variable 'user_uuid' (60% confidence)
-wqflask/wqflask/network_graph/network_graph.py:26: unused import 'gc' (90% confidence)
-wqflask/wqflask/network_graph/network_graph.py:98: unused attribute 'network_data' (60% confidence)
-wqflask/wqflask/news.py:16: unused attribute 'newslist' (60% confidence)
-wqflask/wqflask/search_results.py:121: unused attribute 'json_trait_list' (60% confidence)
-wqflask/wqflask/send_mail.py:41: unused attribute 'From' (60% confidence)
-wqflask/wqflask/send_mail.py:42: unused attribute 'To' (60% confidence)
-wqflask/wqflask/send_mail.py:43: unused attribute 'Subject' (60% confidence)
-wqflask/wqflask/send_mail.py:44: unused attribute 'Body' (60% confidence)
-wqflask/wqflask/show_trait/export_trait_data.py:3: unused import 'operator' (90% confidence)
-wqflask/wqflask/show_trait/SampleList.py:28: unused attribute 'sample_group_type' (60% confidence)
-wqflask/wqflask/show_trait/SampleList.py:29: unused attribute 'header' (60% confidence)
-wqflask/wqflask/show_trait/SampleList.py:66: unused attribute 'this_id' (60% confidence)
-wqflask/wqflask/show_trait/SampleList.py:68: unused attribute 'this_id' (60% confidence)
-wqflask/wqflask/show_trait/show_trait.py:27: unused import 'BasicStatisticsFunctions' (90% confidence)
-wqflask/wqflask/show_trait/show_trait.py:123: unused attribute 'UCSC_BLAT_URL' (60% confidence)
-wqflask/wqflask/show_trait/show_trait.py:124: unused attribute 'UTHSC_BLAT_URL' (60% confidence)
-wqflask/wqflask/show_trait/show_trait.py:126: unused attribute 'UCSC_BLAT_URL' (60% confidence)
-wqflask/wqflask/show_trait/show_trait.py:127: unused attribute 'UTHSC_BLAT_URL' (60% confidence)
-wqflask/wqflask/show_trait/show_trait.py:129: unused attribute 'UCSC_BLAT_URL' (60% confidence)
-wqflask/wqflask/show_trait/show_trait.py:130: unused attribute 'UTHSC_BLAT_URL' (60% confidence)
-wqflask/wqflask/show_trait/show_trait.py:132: unused attribute 'UCSC_BLAT_URL' (60% confidence)
-wqflask/wqflask/show_trait/show_trait.py:133: unused attribute 'UTHSC_BLAT_URL' (60% confidence)
-wqflask/wqflask/show_trait/show_trait.py:135: unused attribute 'UCSC_BLAT_URL' (60% confidence)
-wqflask/wqflask/show_trait/show_trait.py:136: unused attribute 'UTHSC_BLAT_URL' (60% confidence)
-wqflask/wqflask/show_trait/show_trait.py:183: unused attribute 'hddn' (60% confidence)
-wqflask/wqflask/show_trait/show_trait.py:198: unused attribute 'stats_table_width' (60% confidence)
-wqflask/wqflask/show_trait/show_trait.py:198: unused attribute 'trait_table_width' (60% confidence)
-wqflask/wqflask/show_trait/show_trait.py:232: unused attribute 'genofiles' (60% confidence)
-wqflask/wqflask/show_trait/show_trait.py:233: unused attribute 'use_plink_gemma' (60% confidence)
-wqflask/wqflask/show_trait/show_trait.py:234: unused attribute 'use_pylmm_rqtl' (60% confidence)
-wqflask/wqflask/show_trait/show_trait.py:262: unused attribute 'corr_tools' (60% confidence)
-wqflask/wqflask/show_trait/show_trait_page.py:41: unused class 'ShowTraitPage' (60% confidence)
-wqflask/wqflask/show_trait/show_trait_page.py:44: unused attribute 'fd' (60% confidence)
-wqflask/wqflask/show_trait/show_trait_page.py:67: unused variable 'indId' (60% confidence)
-wqflask/wqflask/show_trait/show_trait_page.py:67: unused variable 'indName' (60% confidence)
-wqflask/wqflask/show_trait/show_trait_page.py:138: unused attribute 'display_variance' (60% confidence)
-wqflask/wqflask/show_trait/show_trait_page.py:139: unused attribute 'formID' (60% confidence)
-wqflask/wqflask/tracer.py:37: unused function 'turn_on' (60% confidence)
-wqflask/wqflask/user_manager.py:69: unused function 'add_collection' (60% confidence)
-wqflask/wqflask/user_manager.py:123: unused function 'display_num_collections' (60% confidence)
-wqflask/wqflask/user_manager.py:259: unused attribute 'thank_you_mode' (60% confidence)
-wqflask/wqflask/user_manager.py:299: unused attribute 'registration_info' (60% confidence)
-wqflask/wqflask/user_manager.py:305: unused attribute 'algorithm' (60% confidence)
-wqflask/wqflask/user_manager.py:316: unused attribute 'created_ts' (60% confidence)
-wqflask/wqflask/user_manager.py:411: unused function 'verify_email' (60% confidence)
-wqflask/wqflask/user_manager.py:425: unused function 'password_reset' (60% confidence)
-wqflask/wqflask/user_manager.py:456: unused function 'password_reset_step2' (60% confidence)
-wqflask/wqflask/user_manager.py:497: unused function 'reencode_standalone' (60% confidence)
-wqflask/wqflask/user_manager.py:519: unused function 'github_oauth2' (60% confidence)
-wqflask/wqflask/user_manager.py:549: unused function 'orcid_oauth2' (60% confidence)
-wqflask/wqflask/user_manager.py:606: unused attribute 'login_type' (60% confidence)
-wqflask/wqflask/user_manager.py:691: unused attribute 'successful' (60% confidence)
-wqflask/wqflask/user_manager.py:693: unused attribute 'assumed_by' (60% confidence)
-wqflask/wqflask/user_manager.py:715: unused attribute 'successful' (60% confidence)
-wqflask/wqflask/user_manager.py:719: unused function 'logout' (60% confidence)
-wqflask/wqflask/user_manager.py:730: unused function 'forgot_password' (60% confidence)
-wqflask/wqflask/user_manager.py:735: unused function 'forgot_password_submit' (60% confidence)
-wqflask/wqflask/user_manager.py:755: unused function 'unauthorized' (60% confidence)
-wqflask/wqflask/user_manager.py:770: unused function 'manage_users' (60% confidence)
-wqflask/wqflask/user_manager.py:776: unused function 'manage_user' (60% confidence)
-wqflask/wqflask/user_manager.py:782: unused function 'manage_groups' (60% confidence)
-wqflask/wqflask/user_manager.py:788: unused function 'make_superuser' (60% confidence)
-wqflask/wqflask/user_manager.py:801: unused function 'assume_identity' (60% confidence)
-wqflask/wqflask/user_manager.py:811: unused function 'register' (60% confidence)
-wqflask/wqflask/user_manager.py:921: unused class 'RolesManager' (60% confidence)
-wqflask/wqflask/views.py:17: unused import 'gc' (90% confidence)
-wqflask/wqflask/views.py:23: unused import 'yaml' (90% confidence)
-wqflask/wqflask/views.py:70: unused import 'werkzeug' (90% confidence)
-wqflask/wqflask/views.py:77: unused function 'connect_db' (60% confidence)
-wqflask/wqflask/views.py:82: unused attribute '_database' (60% confidence)
-wqflask/wqflask/views.py:85: unused function 'shutdown_session' (60% confidence)
-wqflask/wqflask/views.py:86: unused variable 'exception' (60% confidence)
-wqflask/wqflask/views.py:98: unused function 'handle_bad_request' (60% confidence)
-wqflask/wqflask/views.py:104: unused variable 'exc_traceback' (60% confidence)
-wqflask/wqflask/views.py:104: unused variable 'exc_type' (60% confidence)
-wqflask/wqflask/views.py:104: unused variable 'exc_value' (60% confidence)
-wqflask/wqflask/views.py:123: unused function 'index_page' (60% confidence)
-wqflask/wqflask/views.py:140: unused function 'tmp_page' (60% confidence)
-wqflask/wqflask/views.py:154: unused function 'cytoscape' (60% confidence)
-wqflask/wqflask/views.py:158: unused function 'twitter' (60% confidence)
-wqflask/wqflask/views.py:178: unused function 'search_page' (60% confidence)
-wqflask/wqflask/views.py:219: unused function 'gsearchact' (60% confidence)
-wqflask/wqflask/views.py:229: unused function 'gsearch_updating' (60% confidence)
-wqflask/wqflask/views.py:241: unused function 'docedit' (60% confidence)
-wqflask/wqflask/views.py:247: unused function 'generated_file' (60% confidence)
-wqflask/wqflask/views.py:252: unused function 'help' (60% confidence)
-wqflask/wqflask/views.py:258: unused function 'wcgna_setup' (60% confidence)
-wqflask/wqflask/views.py:264: unused function 'wcgna_results' (60% confidence)
-wqflask/wqflask/views.py:273: unused function 'ctl_setup' (60% confidence)
-wqflask/wqflask/views.py:279: unused function 'ctl_results' (60% confidence)
-wqflask/wqflask/views.py:288: unused function 'news_route' (60% confidence)
-wqflask/wqflask/views.py:293: unused function 'references' (60% confidence)
-wqflask/wqflask/views.py:299: unused function 'intro' (60% confidence)
-wqflask/wqflask/views.py:304: unused function 'policies' (60% confidence)
-wqflask/wqflask/views.py:309: unused function 'links' (60% confidence)
-wqflask/wqflask/views.py:314: unused function 'environments' (60% confidence)
-wqflask/wqflask/views.py:319: unused function 'submit_trait_form' (60% confidence)
-wqflask/wqflask/views.py:325: unused function 'create_temp_trait' (60% confidence)
-wqflask/wqflask/views.py:335: unused function 'export_trait_excel' (60% confidence)
-wqflask/wqflask/views.py:361: unused function 'export_trait_csv' (60% confidence)
-wqflask/wqflask/views.py:382: unused function 'export_traits_csv' (60% confidence)
-wqflask/wqflask/views.py:394: unused function 'export_perm_data' (60% confidence)
-wqflask/wqflask/views.py:418: unused function 'show_temp_trait_page' (60% confidence)
-wqflask/wqflask/views.py:433: unused function 'show_trait_page' (60% confidence)
-wqflask/wqflask/views.py:448: unused function 'heatmap_page' (60% confidence)
-wqflask/wqflask/views.py:495: unused function 'mapping_results_container_page' (60% confidence)
-wqflask/wqflask/views.py:499: unused function 'loading_page' (60% confidence)
-wqflask/wqflask/views.py:556: unused function 'marker_regression_page' (60% confidence)
-wqflask/wqflask/views.py:696: unused function 'export' (60% confidence)
-wqflask/wqflask/views.py:706: unused function 'export_pdf' (60% confidence)
-wqflask/wqflask/views.py:714: unused variable 'filepath' (60% confidence)
-wqflask/wqflask/views.py:720: unused function 'network_graph_page' (60% confidence)
-wqflask/wqflask/views.py:736: unused function 'corr_compute_page' (60% confidence)
-wqflask/wqflask/views.py:744: unused function 'corr_matrix_page' (60% confidence)
-wqflask/wqflask/views.py:761: unused function 'corr_scatter_plot_page' (60% confidence)
-wqflask/wqflask/views.py:770: unused function 'submit_bnw' (60% confidence)
-wqflask/wqflask/views.py:786: unused function 'get_temp_data' (60% confidence)
-wqflask/wqflask/wgcna/wgcna_analysis.py:5: unused import 'sp' (90% confidence)
-wqflask/wqflask/wgcna/wgcna_analysis.py:18: unused variable 'utils' (60% confidence)
-wqflask/wqflask/wgcna/wgcna_analysis.py:23: unused variable 'r_read_csv' (60% confidence)
-wqflask/wqflask/wgcna/wgcna_analysis.py:24: unused variable 'r_dim' (60% confidence)
-wqflask/wqflask/wgcna/wgcna_analysis.py:27: unused variable 'r_paste' (60% confidence)
-wqflask/wqflask/wgcna/wgcna_analysis.py:33: unused variable 'r_matrix' (60% confidence)
-wqflask/wqflask/wgcna/wgcna_analysis.py:34: unused variable 'r_seq' (60% confidence)
-wqflask/wqflask/wgcna/wgcna_analysis.py:36: unused variable 'r_names' (60% confidence)
-wqflask/wqflask/wgcna/wgcna_analysis.py:37: unused variable 'r_sink' (60% confidence)
-wqflask/wqflask/wgcna/wgcna_analysis.py:38: unused variable 'r_is_NA' (60% confidence)
-wqflask/wqflask/wgcna/wgcna_analysis.py:39: unused variable 'r_file' (60% confidence)