search

isabelrem / 2023-Software-Development-Assessment

MIT License
2 stars 1 forks source link

Implementing bed changes in issue #56 #57

Closed TomLivesey-UoM closed 9 months ago

TomLivesey-UoM commented 9 months ago

Implemented the bullet points found in issue #56 - improvements to bed files after discussion w/ users.

jess789550 commented 9 months ago

If you would like to search by R-code, enter 1. If you would like to enter a disease description, enter 2. 1 Enter your search term: (e.g., R128 or pneumothorax) R128 Which genome build would you like to use? Enter 1 for GRCh37. Enter 2 for GRCh38. 1 2023-12-21 08:49:48,003 INFO: Starting PanelSearch with input type: R-code GRch37 build selected. Panel ID: 13 Panel Name: Brugada syndrome and cardiac sodium channel disease GMS Sign-off Status: Signed Off Associated NGTD R-codes: R128 Gene Number: 23 Gene List: HGNC_ID Symbol Coords Mane_Select_Transcript HGNC:10593 SCN5A 3:38589548-38691164 NM_000335.5 HGNC:6251 KCNH2 7:150642049-150675403 NM_000238.4 HGNC:60 ABCC9 12:21950335-22094336 NM_020297.4 HGNC:493 ANK2 4:113739265-114304896 NM_001148.6 HGNC:1390 CACNA1C 12:2079952-2802108 NM_000719.7 HGNC:1399 CACNA2D1 7:81575760-82073114 NM_000722.4 HGNC:1402 CACNB2 10:18429606-18830798 NM_201596.3 HGNC:1529 CAV3 3:8775486-8883492 NM_033337.3 HGNC:2900 DLG1 3:196769431-197026171 NM_001366207.1 HGNC:28956 GPD1L 3:32147181-32210205 NM_015141.4 HGNC:16882 HCN4 15:73612200-73661605 NM_005477.3 HGNC:6239 KCND3 1:112313284-112531777 NM_001378969.1 HGNC:6243 KCNE3 11:74165886-74178774 NM_005472.5 HGNC:6241 KCNE5 X:108866929-108868393 NM_012282.4 HGNC:6269 KCNJ8 12:21917889-21928515 NM_004982.4 HGNC:9024 PKP2 12:32943679-33049774 NM_001005242.3 HGNC:17679 RANGRF 17:8191815-8193410 NM_016492.5 HGNC:10582 SCN10A 3:38738293-38835501 NM_006514.4 HGNC:10586 SCN1B 19:35521588-35531352 NM_001037.5 HGNC:10589 SCN2B 11:118032666-118047388 NM_004588.5 HGNC:20665 SCN3B 11:123499895-123525952 NM_001040151.2 HGNC:16643 SLMAP 3:57741177-57914895 NM_001377540.1 HGNC:17993 TRPM4 19:49660998-49715093 NM_017636.4 2023-12-21 08:49:50,698 INFO: Panel data processed successfully Generate BED file? (Y/N) Y For exon coordinates on transcript, press '1'. For genomic coordinates, press '2'. 1 Standard +/- 5 bp padding used in beds file for exon - enter a number between 0-15 to change this. Otherwise press enter.10 2023-12-21 08:50:14,355 INFO Using a padding value of +/- 10 bp. 2023-12-21 08:50:14,358 DEBUG JSON data parsed successfully. 2023-12-21 08:50:14,363 INFO BED and JSON files written successfully. 2023-12-21 08:50:14,368 INFO: BED file generation initiated Would you like to save this search against a patient ID? (Y/N) Y What patient ID would you like to save this search against? testeroo Brugada syndrome and cardiac sodium channel disease GRch37 Traceback (most recent call last): File "/home/jessicak/PycharmProjects/2023-Software-Development-Assessment/PanelSearch/main.py", line 148, in main() File "/home/jessicak/PycharmProjects/2023-Software-Development-Assessment/PanelSearch/main.py", line 135, in main create_sql_record(panel_name,SEARCH.genome_build, pid) File "/home/jessicak/PycharmProjects/2023-Software-Development-Assessment/PanelSearch/main.py", line 81, in create_sql_record PK_Parse_Data_to_SQL_cloud(pid,genome_build,PK = panel_name) File "/home/jessicak/PycharmProjects/2023-Software-Development-Assessment/PanelSearch/API_to_SQL_cloud.py", line 11, in PK_Parse_Data_to_SQL_cloud result = PanelApp_Request_Parse.panelapp_search_parse(response.json(), genome_build) NameError: name 'PanelApp_Request_Parse' is not defined. Did you mean: 'panelapp_search_parse'?

^ error fixed in logging enhancement branch #53