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ben-silke / biol3209

This repo contains the code for the undertaking of the biol3209 subject.
BSD 3-Clause "New" or "Revised" License
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csv gene names #26

Closed ben-silke closed 1 year ago

ben-silke commented 2 years ago

[("['dnaA']", 352), ("['dnaN']", 270), ("['recF']", 188), ("['gyrB']", 143), ("['yaaA']", 67), ("['gyrA']", 35), ("['gnd']", 24), ("['thrA']", 17), ("['thrC']", 17), ("['thrB']", 17), ("['thrL']", 16), ("['mioC']", 12), ("['yidA']", 11), ("['ravA']", 10), ("['asnC']", 10), ("['viaA']", 10), ("['kup']", 10), ("['rpmH']", 8), ("['rnpA']", 7), ("['yidD']", 6), ("['obgE']", 6), ("['mnmG']", 6), ("['rpsT']", 6), ("['yaaI']", 6), ("['mog']", 5), ("['asnA']", 5), ("['dnaJ']", 5), ("['dnaK']", 5), ("['satP']", 5), ("['yaaX']", 5), ("['rbsD']", 5), ("['hemE']", 5), ("['msyB']", 5), ("['rbsK']", 5), ("['yaaJ']", 5), ("['dgoR']", 4), ("['glmS']", 4), ("['nadD']", 4), ("['ruvC']", 4), ("['ovoA']", 4), ("['tal']", 4), ("['rplA']", 3), ("['holB']", 3), ("['glmU']", 3), ("['yidB']", 3), ("['eno']", 3), ("['pabC']", 3), ("['yidC']", 3), ("['tyrS']", 3), ("['rlmB']", 3), ("['rpoB']", 3), ("['rpoC']", 3), ("['rplL']", 3), ("['rlbA']", 3), ("['rplK']", 3), ("['rsmG']", 3), ("['tmk']", 3), ("['nusG']", 3), ("['rplJ']", 3), ("['cdaR']", 2), ("['rplC']", 2), ("['rlmG']", 2), ("['tufA']", 2), ("['rplQ']", 2), ("['rfaD']", 2), ("['plsY']", 2), ("['ridA']", 2), ("['ispF']", 2), ("['glpT']", 2), ("['pabA']", 2), ("['murP']", 2), ("['gmhB']", 2), ("['pssA']", 2), ("['glnL']", 2), ("['ybfB']", 2), ("['hemB']", 2), ("['rrf']", 2), ("['phoU']", 2), ("['ybdN']", 2), ("['rsmA']", 2), ("['hslO']", 2), ("['alkA']", 2), ("['pth']", 2), ("['remB']", 2), ("['ahpF']", 2), ("['psd']", 2), ("['aroB']", 2), ("['atpI']", 2), ("['dnaX']", 2), ("['pstC']", 2), ("['glyS']", 2), ("['ybdJ']", 2), ("['xseB']", 2), ("['ybfO']", 2), ("['hemC']", 2), ("['murR']", 2), ("['rpsQ']", 2), ("['ybcH']", 2), ("['truA']", 2), ("['gltP']", 2), ("['nhaR']", 2), ("['pabB']", 2), ("['purT']", 2), ("['ybeF']", 2), ("['tilS']", 2), ("['rpsJ']", 2), ("['ybfQ']", 2), ("['mfd']", 2), ("['atpD']", 2), ("['ilvE']", 2), ("['lysS']", 2), ("['mokC']", 2), ("['ybfA']", 2), ("['recR']", 2), ("['csgA']", 2), ("['gudD']", 2), ("['ybdO']", 2), ("['rbsC']", 2), ("['fusA']", 2), ("['istB']", 2), ("['atpE']", 2), ("['ybdK']", 2), ("['yacL']", 2), ("['ispD']", 2), ("['qseC']", 2), ("['rbsA']", 2), ("['glyQ']", 2), ("['rplR']", 2), ("['rpsI']", 2), ("['nagZ']", 2), ("['rplM']", 2), ("['rpsG']", 2), ("['purB']", 2), ("['ybaK']", 2), ("['rpmJ']", 2), ("['waaA']", 2), ("['rpsE']", 2), ("['murA']", 2), ("['rpmC']", 2), ("['ycbJ']", 2), ("['glmM']", 2), ("['mnmE']", 2), ("['pyk']", 2), ("['atpH']", 2), ("['rpsS']", 2), ("['ybfI']", 2), ("['pstB']", 2), ("['pstA']", 2), ("['infA']", 2), ("['dacA']", 2), ("['rplO']", 2), ("['adk']", 2), ("['cybC']", 2), ("['xseA']", 2), ("['ybdG']", 2), ("['rplB']", 2), ("['ybfF']", 2), ("['secY']", 2), ("['rpsF']", 2), ("['ssb']", 2), ("['rpsR']", 2), ("['dusB']", 2), ("['dbpA']", 2), ("['gltX']", 2), ("['serS']", 2), ("['rpsL']", 2), ("['lptA']", 2), ("['garD']", 2), ("['ybcF']", 2), ("['ybbJ']", 2), ("['glsA']", 2), ("['rplW']", 2), ("['cysS']", 2), ("['rplV']", 2), ("['hslR']", 2), ("['atpC']", 2), ("['cas2']", 2), ("['rpsK']", 2), ("['secE']", 2), ("['murQ']", 2), ("['bfr']", 2), ("['rpsH']", 2), ("['ybdM']", 2), ("['ybfP']", 2), ("['rpoA']", 2), ("['insI2']", 2), ("['rpsC']", 2), ("['rsmI']", 2), ("['aroA']", 2), ("['atpA']", 2), ("['rplX']", 2), ("['atpF']", 2), ("['fabF']", 2), ("['ybcL']", 2), ("['folP']", 2), ("['ybfG']", 2), ("['ispE']", 2), ("['aroK']", 2), ("['rplD']", 2), ("['radA']", 2), ("['gudP']", 2), ("['atpB']", 2), ("['ruvA']", 2), ("['tsaD']", 2), ("['ybbC']", 2), ("['atpG']", 2), ("['rpmD']", 2), ("['ybcM']", 2), ("['rnr']", 2), ("['garR']", 2), ("['waaF']", 2), ("['prs']", 2), ("['rplE']", 2), ("['rbsB']", 2), ("['rpiB']", 2), ("['rplP']", 2), ("['istA']", 2), ("['folK']", 2), ("['ybcI']", 2), ("['nhaA']", 2), ("['ribD']", 2), ("['hflX']", 2), ("['mltG']", 2), ("['tadA']", 2), ("['purR']", 2), ("['guaB']", 2), ("['ftsH']", 2), ("['rplF']", 2), ("['yabR']", 2), ("['cysE']", 2), ("['abrB']", 2), ("['repB']", 2), ("['rbsR']", 2), ("['cysK']", 2), ("['pstS']", 2), ("['nadC']", 2), ("['folB']", 2), ("['rpsM']", 2), ("['repA']", 2)]

ben-silke commented 2 years ago

counts_stats.csv high_counts_stats.csv

ben-silke commented 1 year ago

for 'kup' {'GeneID:9731391': ['10552at91347', '449at1903410', '104332at1224', '26039at1236', '589903at2'], 'GeneID:948255': {'status': 'ok', 'message': None, 'data': [], 'count': 0, 'skip': 0, 'limit': 1000, 'query': '948255', 'level': None, 'url': 'https://www.orthodb.org//search?query=948255&ncbi=1', 'universal': None, 'singlecopy': None, 'inclusive': 1}, 'GeneID:8914772': ['677at1903409', '104332at1224', '589903at2', '10552at91347', '346at551', '26039at1236']}

ben-silke commented 1 year ago

endpoints = get_gene('viaA')

{'GeneID:9731389': ['576118at2', '13705at91347', '534689at1224', '1129at1903410', '237305at1236'], 'GeneID:948257': {'status': 'ok', 'message': None, 'data': [], 'count': 0, 'skip': 0, 'limit': 1000, 'query': '948257', 'level': None, 'url': 'https://www.orthodb.org//search?query=948257&ncbi=1', 'universal': None, 'singlecopy': None, 'inclusive': 1}, 'GeneID:8911190': ['2869at1903409', '13705at91347', '534689at1224', '576118at2', '237305at1236', '1197at551']}

ben-silke commented 1 year ago

____ Gene Name === thrA {'GeneID:6803166': [], 'GeneID:1251520': [], 'GeneID:945803': []} ____ Gene Name === thrC {'GeneID:6801127': [], 'GeneID:1251522': [], 'GeneID:945198': []} ____ Gene Name === thrB {'GeneID:6801079': [], 'GeneID:1251521': [], 'GeneID:947498': []} ____ Gene Name === thrL {'GeneID:1251519': [], 'GeneID:944742': []} ____ Gene Name === mioC {'GeneID:9735696': ['317369at1236', '1961680at2', '5980at1903410', '73261at91347', '860985at1224'], 'GeneID:948249': [], 'GeneID:8911189': ['4948at551', '860985at1224', '317369at1236', '73261at91347', '1961680at2', '9987at1903409']} ____ Gene Name === yidA {'GeneID:57664817': [], 'GeneID:948204': []} ____ Gene Name === ravA {'GeneID:9731390': ['895310at2', '1196at1903410', '15781at91347', '349739at1224', '160935at1236'], 'GeneID:948256': [], 'GeneID:8914771': ['703at551', '160935at1236', '895310at2', '1532at1903409', '15781at91347', '349739at1224']} ____ Gene Name === asnC {'GeneID:9731388': ['75663at91347', '726288at1224', '1844486at2', '6124at1903410', '308580at1236'], 'GeneID:948259': [], 'GeneID:8913324': ['75663at91347', '4718at551', '9376at1903409', '726288at1224', '1844486at2', '308580at1236']}

ben-silke commented 1 year ago

____ Gene Name === dnaN {'GeneID:45123507': [], 'GeneID:57664814': [], 'GeneID:41354801': [], 'GeneID:55589809': [], 'GeneID:67387780': [], 'GeneID:8829629': [], 'GeneID:29760340': ['81268at80840', '18248at119060', '1040142at2', '1094at106589', '102085at28216', '774596at1224'], 'GeneID:5707575': ['1040142at2', '129617at201174', '97662at1760', '1899at28056'], 'GeneID:45232534': [], 'GeneID:879244': [], 'GeneID:44996475': [], 'GeneID:58015568': [], 'GeneID:61130860': [], 'GeneID:3788685': [], 'GeneID:31488959': ['10470at31989', '58406at28211', '1040142at2', '415at1060', '11462at204455', '774596at1224'], 'GeneID:9380389': [], 'GeneID:45093089': [], 'GeneID:45020036': [], 'GeneID:948218': [], 'GeneID:939970': [], 'GeneID:7410563': ['8813at29547', '8050at213849', '3062at72294', '2008at194', '1040142at2', '17355at68525', '774596at1224'], 'GeneID:32489329': ['1376at1637', '122677at91061', '67485at1385', '1040142at2', '112162at1239', '1378at186820'], 'GeneID:45040439': [], 'GeneID:3433715': ['1040142at2', '4654at1716', '129617at201174', '24240at85007', '97662at1760']} ____ Gene Name === recF {'GeneID:45123508': [], 'GeneID:57664815': [], 'GeneID:55589810': [], 'GeneID:8829630': [], 'GeneID:5707577': ['2427at28056', '190591at201174', '180056at1760', '891841at2'], 'GeneID:45232535': [], 'GeneID:879229': [], 'GeneID:44996477': [], 'GeneID:58015569': [], 'GeneID:61130861': [], 'GeneID:3786823': [], 'GeneID:31488960': ['21010at204455', '16437at31989', '896at1060', '891841at2', '421736at1224', '187977at28211'], 'GeneID:9380390': [], 'GeneID:45020038': [], 'GeneID:948209': [], 'GeneID:939454': [], 'GeneID:45040440': [], 'GeneID:3431931': ['30340at85007', '190591at201174', '180056at1760', '5777at1716', '891841at2']} ____ Gene Name === gyrB {'GeneID:57664816': [], 'GeneID:8829631': [], 'GeneID:29760320': ['1109at119060', '205481at2', '84241at1224', '4233at28216', '4029at80840', '73at106589'], 'GeneID:45232536': [], 'GeneID:879230': [], 'GeneID:58015570': [], 'GeneID:31488961': ['205481at2', '34at1060', '1135at204455', '1055at31989', '84241at1224', '12596at28211'], 'GeneID:9380391': [], 'GeneID:45093090': [], 'GeneID:45020039': [], 'GeneID:948211': [], 'GeneID:939456': [], 'GeneID:7410564': ['205481at2', '540at29547', '217at72294', '84241at1224', '1577at68525', '663at213849', '150at194'], 'GeneID:45040441': []} ____ Gene Name === yaaA {'GeneID:44996476': [], 'GeneID:45020037': [], 'GeneID:944749': []} ____ Gene Name === gyrA {'GeneID:45020040': [], 'GeneID:946614': [], 'GeneID:940002': []} ____ Gene Name === gnd {'GeneID:5707576': ['3834at28056', '155029at1760', '1245550at2', '159831at201174'], 'GeneID:946554': []}

ben-silke commented 1 year ago

high_cds_counts_stats.csv cds_counts_stats.csv

ben-silke commented 1 year ago

closed as tasks completed