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Insert 1bp #13
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,114 @@ | ||
| import csv | ||
| import sys | ||
| import hgvs | ||
| import hgvs.utils | ||
| #from hgvs import utils | ||
| #import pygr | ||
| from pygr.seqdb import SequenceFileDB | ||
| from flask import Flask,jsonify, request | ||
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| application = app = Flask(__name__) | ||
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| genome = SequenceFileDB('/Users/afrieden/test/hg/hg18.fa') | ||
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| geneTranscripts = {'CFTR':'NM_000492.3','PCDH15':'NM_033056.3','ABCC8':'NM_000352.3','ASPA':'NM_000049.2','BCKDHA':'NM_000709.3','BCKDHB':'NM_000056.3', | ||
| 'BLM':'NM_000057.2','CLRN1':'NM_174878.2','DLD':'NM_000108.3','FANCC':'NM_000136.2','G6PC':'NM_000151.3','HEXA':'NM_000520.4', | ||
| 'IKBKAP':'NM_003640.3', | ||
| 'MCOLN1':'NM_020533.2', | ||
| 'SMPD1':'NM_000543.4', | ||
| 'TMEM216':'NM_001173990.2', | ||
| 'FKTN':'NM_006731.2', | ||
| 'GBA':'NM_001005741.2', | ||
| 'NEB':'NM_001164507.1'} | ||
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| def getGeneFromPosition(_position): | ||
| #check which gene it is in | ||
| geneExportPath = '/Users/afrieden/Projects/hgvs/hgvs/data/geneExport.csv' | ||
| reader = csv.reader(open(geneExportPath), delimiter=',') | ||
| next(reader, None) | ||
| contents = [line for line in reader] | ||
| position = int(_position) | ||
| for row in contents: | ||
| if(position > int(row[1])): | ||
| if(position < int(row[2])): | ||
| return row[0] | ||
| _max = sys.maxint | ||
| closestGene = '' | ||
| for row in contents: | ||
| diff_start = abs(int(row[1])-position) | ||
| diff_end = abs(int(row[2]) - position) | ||
| diff = min(diff_start,diff_end) | ||
| if(diff < _max): | ||
| _max = diff | ||
| closestGene = row[0] | ||
| return closestGene | ||
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| with open('./hgvs/data/gsg-transcript-03-06-2014.txt') as infile: | ||
| transcripts = hgvs.utils.read_transcripts(infile) | ||
| #transcripts = read_transcripts(infile) | ||
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| def get_transcript(name): | ||
| return transcripts.get(name) | ||
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| @app.route('/') | ||
| def index(): | ||
| return jsonify( { | ||
| 'first':'http://localhost:5000/convert/cdnaToVcf?gene=CFTR&cdna=c.1521_1523delCTT', | ||
| 'second':'http://localhost:5000/convert/vcfToCdna?chrom=chr7&pos=116986880&ref=ATCT&alt=A' | ||
| }) | ||
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| @app.route('/convert/vcfToCdna') | ||
| def vcfToCdna(): | ||
| _chrom = str(request.args.get('chrom')) | ||
| _pos = int(request.args.get('pos')) | ||
| _ref = str(request.args.get('ref')) | ||
| _alt = str(request.args.get('alt')) | ||
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| chrom, offset, ref, alt = (_chrom, _pos, _ref, _alt) | ||
| gene = str(getGeneFromPosition(_pos)) | ||
| transcript = get_transcript(geneTranscripts[gene]) | ||
| hgvs_name = hgvs.format_hgvs_name( | ||
| chrom, offset, ref, alt, genome, transcript) | ||
| cdnaName = hgvs_name.split(':')[1] | ||
| fullName = gene + ':' + cdnaName | ||
| return jsonify( {'name':fullName}) | ||
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| @app.route('/convert/cdnaToVcf') | ||
| def cdnaToVcf(): | ||
| gene = request.args.get('gene') | ||
| cdna_name = request.args.get('cdna') | ||
| transcript = geneTranscripts[gene] | ||
| transcriptName = str(transcript + ':' + cdna_name) | ||
| chrom, offset, ref, alt = hgvs.parse_hgvs_name( | ||
| transcriptName, genome, get_transcript=get_transcript) | ||
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| return jsonify({ | ||
| 'foundTranscript': transcript, | ||
| 'geneInput':gene, | ||
| 'cdna_name':cdna_name, | ||
| 'transcriptName':transcriptName, | ||
| 'chrom':chrom, | ||
| 'position':offset, | ||
| 'ref':ref, | ||
| 'alt':alt | ||
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| }) | ||
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| if __name__ == '__main__': | ||
| app.run(debug = True) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| geneName,geneLower,geneUpper | ||
| BCKDHA,46595573,46622353 | ||
| IKBKAP,110671216,110733247 | ||
| CLRN1,152128413,152173185 | ||
| BLM,89091627,89159513 | ||
| HEXA,70423472,70455367 | ||
| BCKDHB,80873130,81110240 | ||
| CFTR,116907385,117094398 | ||
| PCDH15,55251624,56094028 | ||
| ASPA,3326204,3349132 | ||
| G6PC,38306420,38316969 | ||
| DLD,107318932,107346940 | ||
| SMPD1,6368405,6372413 | ||
| MCOLN1,7493637,7504681 | ||
| HBB,5203404,5204827 | ||
| ABCC8,17371114,17454899 | ||
| FANCC,96903810,97051394 | ||
| GBA,153471410,153477527 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| 184 NM_000492.3 chr7 + 116907384 117094398 116907384 117094398 27 116907384,116931542,116936323,116958188,116961565,116962537,116963837,116967389,116969305,116975930,116986753,117015028,117017642,117019223,117022219,117030115,117030821,117033963,117037808,117038870,117041902,117054811,117069727,117080131,117091977,117092748,117094197, 116907437,116931653,116936432,116958404,116961655,116962701,116963963,116967636,116969398,116976113,116986945,117015123,117017729,117019947,117022348,117030153,117031072,117034043,117037959,117039098,117042003,117055060,117069883,117080221,117092150,117092854,117094398, 0 cmpl cmpl 0,2,2,0,0,0,2,2,0,0,0,0,2,2,0,0,2,1,0,1,1,0,0,0,0,2,0, | ||
| 126 NM_033056.3 chr10 - 55251623 56094028 55251623 56094028 32 55251623,55257158,55258330,55261080,55270085,55286940,55296407,55333008,55368580,55370631,55389497,55391517,55425414,55449957,55452657,55496522,55509096,55519749,55562640,55582865,55613209,55614899,55625448,55643701,55666588,55747036,55759361,55776130,55798885,55808547,55957577,56093937, 55253124,55257314,55258339,55261299,55270262,55287029,55296623,55333136,55368721,55370741,55389610,55391658,55425531,55450182,55452963,55496651,55509190,55519829,55562773,55583059,55613359,55615034,55625655,55643814,55666697,55747207,55759472,55776250,55799041,55808708,55957643,56094028, 0 cmpl cmpl 2,2,2,2,2,0,0,1,1,2,0,0,0,0,0,0,2,0,2,0,0,0,0,1,0,0,0,0,0,1,1,0, | ||
| 89 NM_000352.3 chr11 - 17371113 17454899 17371113 17454899 39 17371113,17371819,17372388,17373294,17373732,17373974,17375038,17375315,17375806,17376461,17380783,17382634,17383616,17384744,17385010,17385476,17386514,17388638,17390788,17391516,17392634,17393426,17395052,17405171,17405989,17406411,17406687,17408936,17410326,17420842,17421300,17426638,17431241,17438610,17439705,17441560,17448223,17453008,17454751, 17371251,17371882,17372522,17373398,17373841,17374053,17375169,17375436,17375920,17376564,17380876,17382792,17383686,17384911,17385252,17385576,17386640,17388776,17390869,17391601,17392733,17393462,17395085,17405277,17406065,17406528,17406793,17409082,17410367,17421005,17421435,17426794,17431406,17438799,17439948,17441727,17448345,17453150,17454899, 0 cmpl cmpl 0,0,1,2,1,0,1,0,0,2,2,0,2,0,1,0,0,0,0,2,2,2,2,1,0,0,2,0,1,0,0,0,0,0,0,1,2,1,0, | ||
| 610 NM_000049.2 chr17 + 3326203 3349132 3326203 3349132 6 3326203,3331646,3333542,3339278,3344393,3348934, 3326439,3331842,3333636,3339386,3344503,3349132, 0 cmpl cmpl 0,2,0,1,1,0, | ||
| 904 NM_000709.3 chr19 + 46595572 46622353 46595572 46622353 9 46595572,46608381,46608667,46611793,46616879,46619908,46620373,46620742,46622182, 46595680,46608561,46608754,46611902,46617041,46620115,46620515,46620914,46622353, 0 cmpl cmpl 0,0,0,0,1,1,1,2,0, | ||
| 150 NM_000056.3 chr6 + 80873129 81110240 80873129 81110240 10 80873129,80893982,80895596,80934113,80935310,80937717,80967369,80969537,81039570,81110099, 80873325,80894060,80895665,80934247,80935466,80937826,80967467,80969648,81039657,81110240, 0 cmpl cmpl 0,1,1,1,0,0,1,0,0,0, | ||
| 160 NM_000057.2 chr15 + 89091626 89159513 89091626 89159513 21 89091626,89093600,89096020,89099044,89104380,89104827,89107199,89109529,89111143,89113366,89113671,89127055,89129154,89134882,89138400,89142423,89147754,89148400,89153370,89155438,89159335, 89091724,89094301,89096180,89099172,89104513,89105489,89107391,89109648,89111257,89113465,89113820,89127162,89129315,89135078,89138591,89142571,89147954,89148593,89153493,89155640,89159513, 0 cmpl cmpl 0,2,1,2,1,2,1,1,0,0,0,2,1,0,1,0,1,0,1,1,2, | ||
| 1734 NM_174878.2 chr3 - 152128412 152173185 152128412 152173185 3 152128412,152142058,152172932, 152128678,152142238,152173185, 0 cmpl cmpl 1,1,0, | ||
| 1500 NM_000198.3 chr7 + 107318931 107346940 107318931 107346940 14 107318931,107320880,107329418,107330005,107331158,107332638,107333041,107333947,107343186,107344474,107344953,107345604,107346690,107346874, 107318970,107320959,107329498,107330074,107331228,107332739,107333185,107334049,107343377,107344645,107345143,107345742,107346780,107346940, 0 cmpl cmpl 0,0,1,0,0,1,0,0,0,2,2,0,0,0, | ||
| 166 NM_000136.2 chr9 - 96903809 97051394 96903809 97051394 14 96903809,96909168,96913565,96916731,96919417,96927188,96928631,96937448,96952025,96973181,96974139,97042751,97049534,97051229, 96903953,96909372,96913740,96916813,96919493,96927288,96928684,96937605,96952190,96973246,96974250,97042846,97049619,97051394, 0 cmpl cmpl 0,0,2,1,0,2,0,2,2,0,0,1,0,0, | ||
| 898 NM_000151.3 chr17 + 38306419 38316969 38306419 38316969 5 38306419,38309473,38313065,38314845,38316457, 38306649,38309583,38313171,38314961,38316969, 0 cmpl cmpl 0,2,1,2,1, | ||
| 1139 NM_000520.4 chr15 - 70423471 70455367 70423471 70455367 14 70423471,70424840,70425629,70425921,70427080,70427442,70428473,70429912,70430527,70432462,70433085,70434953,70435919,70455114, 70423535,70424945,70425720,70426105,70427153,70427529,70428654,70430045,70430629,70432573,70433132,70435019,70436012,70455367, 0 cmpl cmpl 2,2,1,0,2,2,1,0,0,0,1,1,1,0, | ||
| 179 NM_003640.3 chr9 - 110671215 110733247 110671215 110733247 36 110671215,110676995,110680095,110680723,110681546,110682152,110683805,110684225,110691432,110693303,110695086,110696043,110698596,110699053,110699248,110700602,110700771,110701922,110702360,110703525,110703728,110704939,110705663,110708403,110710405,110713110,110714364,110718304,110719647,110720911,110721353,110724942,110728623,110729472,110731869,110733097, 110671283,110677071,110680250,110680851,110681658,110682266,110683866,110684288,110691494,110693505,110695184,110696167,110698745,110699139,110699386,110700682,110700850,110701996,110702476,110703631,110703782,110705043,110705770,110708586,110710505,110713281,110714595,110718398,110719771,110721002,110721450,110725028,110728704,110729554,110732022,110733247, 0 cmpl cmpl 1,0,1,2,1,1,0,0,1,0,1,0,1,2,2,0,2,0,1,0,0,1,2,2,1,1,1,0,2,1,0,1,1,0,0,0, | ||
| 642 NM_020533.2 chr19 + 7493636 7504681 7493636 7504681 14 7493636,7495846,7497324,7497646,7498405,7498749,7499043,7499482,7499706,7499986,7500475,7501171,7504408,7504644, 7493667,7496052,7497492,7497812,7498514,7498846,7499143,7499589,7499856,7500088,7500598,7501387,7504539,7504681, 0 cmpl cmpl 0,1,0,0,1,2,0,1,0,0,0,0,0,2, | ||
| 633 NM_000543.4 chr11 + 6368404 6372413 6368404 6372413 6 6368404,6369189,6371021,6371422,6371701,6372003, 6368722,6369962,6371193,6371499,6371847,6372413, 0 cmpl cmpl 0,0,2,0,2,1, | ||
| 1051 NM_001173990.2 chr11 + 60916679 60922324 60916679 60922324 5 60916679,60917278,60917931,60921821,60922317, 60916713,60917380,60918024,60922023,60922324 0 cmpl cmpl 0,1,1,1,2, | ||
| 176 NM_001079802.1 chr9 + 107377134 107437366 107377134 107437366 9 107377134,107398699,107403246,107406316,107409920,107417379,107420060,107422035,107437152, 107377239,107398759,107403450,107406594,107410053,107417509,107420194,107422163,107437366, 0 cmpl cmpl 0,0,0,0,2,0,1,0,2, | ||
| 1769 NM_001005741.2 chr1 - 153471409 153477527 153471409 153477527 11 153471409,153471609,153472095,153472659,153473755,153474548,153474931,153476030,153476300,153477044,153477500, 153471515,153471726,153472259,153472884,153473993,153474721,153475065,153476177,153476492,153477132,153477527, 0 cmpl cmpl 2,2,0,0,2,0,1,1,1,0,0, | ||
| 218 NM_001164507.1 chr2 - 152050519 152297916 152050519 152297916 180 152050519,152054730,152055131,152056442,152056857,152057146,152058112,152058534,152058920,152061035,152061700,152062385,152063019,152064057,152066150,152067552,152068108,152070237,152070925,152071668,152072764,152077492,152078339,152079077,152079577,152081218,152083077,152083724,152084417,152089070,152089274,152089922,152090717,152090917,152091677,152092240,152093969,152095753,152096551,152098974,152100450,152101891,152102631,152102899,152105103,152105456,152106206,152110647,152111104,152112188,152112393,152113067,152114395,152116497,152117431,152118157,152118587,152119690,152125351,152125763,152125967,152126869,152127370,152128365,152128582,152129803,152130260,152130475,152131927,152132830,152133075,152133377,152134027,152134840,152135256,152140454,152140910,152144097,152145556,152146242,152147223,152148214,152150266,152151164,152152133,152154648,152156107,152156793,152157775,152158766,152160819,152161717,152162686,152165201,152166660,152167346,152168328,152169319,152171365,152172263,152173232,152174568,152175275,152175521,152176945,152179035,152180761,152182123,152183034,152184210,152185678,152190293,152191761,152192282,152194298,152195474,152195902,152198413,152200986,152204039,152204616,152205114,152207333,152207524,152207909,152208577,152209227,152210889,152214935,152215333,152218751,152220029,152220576,152220912,152222742,152223824,152226894,152228307,152229260,152229518,152230092,152230849,152232563,152233786,152235782,152237128,152239236,152240046,152242324,152242635,152244480,152244677,152245489,152247421,152249537,152252178,152252385,152253051,152255486,152256623,152256818,152257020,152259082,152259281,152260337,152261396,152261907,152262109,152262303,152271640,152274415,152275193,152282175,152288141,152289019,152289616,152290212,152292450,152294374,152297880, 152050693,152054837,152055278,152056535,152057041,152057254,152058205,152058627,152059013,152061128,152061793,152062478,152063112,152064150,152066243,152067645,152068201,152070330,152071018,152071773,152072869,152077597,152078453,152079188,152079688,152081323,152083182,152083829,152084528,152089175,152089376,152090033,152090828,152091022,152091782,152092345,152094074,152095861,152096656,152099079,152100555,152101996,152102736,152103004,152105208,152105561,152106311,152110758,152111203,152112293,152112498,152113175,152114500,152116605,152117536,152118262,152118785,152119804,152125459,152125868,152126072,152126974,152127568,152128479,152128690,152129908,152130365,152130580,152132239,152132938,152133177,152133476,152134132,152135152,152135361,152140559,152141114,152144409,152145664,152146347,152147427,152148526,152150374,152151269,152152337,152154960,152156215,152156898,152157979,152159078,152160927,152161822,152162890,152165513,152166768,152167451,152168532,152169631,152171473,152172368,152173436,152174880,152175383,152175626,152177149,152179347,152180869,152182228,152183238,152184522,152185786,152190398,152191965,152192594,152194406,152195579,152196106,152198725,152201094,152204144,152204820,152205426,152207441,152207629,152208113,152208889,152209335,152210994,152215139,152215645,152218859,152220134,152220783,152221224,152222850,152223929,152227101,152228619,152229368,152229623,152230299,152231161,152232671,152233891,152235989,152237440,152239344,152240151,152242531,152242947,152244588,152244782,152245588,152247529,152249735,152252292,152252493,152253156,152255585,152256728,152256926,152257122,152259196,152259389,152260442,152261495,152262012,152262217,152262408,152271757,152274523,152275298,152282280,152288246,152289124,152289721,152290320,152292666,152294416,152297916, 0 cmpl cmpl 0,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, |
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Thanks for this contribution!
Do you think this could be done as a separate package that imports the hgvs library? Majority of use cases will require just the library, not the HTTP API.
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Ho @pkaleta totally agree, I can put this as a separate one. When I originally wrote this it was because our pipeline was primarily java and wanted a way to interact with this. Alternatively this can be a multi-package project. Up to you.
Let me know.