From 5384fe93315bb5a2e638603bf7ab5ff8d4476193 Mon Sep 17 00:00:00 2001 From: Vladyslav Levchenko Date: Tue, 10 Sep 2024 16:56:23 +0300 Subject: [PATCH] updated pipeline.ipynb to prevent conflict --- tests/pipeline.ipynb | 4090 ++---------------------------------------- 1 file changed, 173 insertions(+), 3917 deletions(-) diff --git a/tests/pipeline.ipynb b/tests/pipeline.ipynb index 9a1aa3c..e85aff1 100644 --- a/tests/pipeline.ipynb +++ b/tests/pipeline.ipynb @@ -2,3902 +2,227 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, "id": "initial_id", "metadata": { - "ExecuteTime": { - "end_time": "2024-05-13T15:38:18.029744Z", - "start_time": "2024-05-13T15:38:17.807980Z" - }, "collapsed": true, "jupyter": { "outputs_hidden": true } }, - "outputs": [], "source": [ "import pandas as pd\n", + "import requests\n", "\n", "from api.data import (store_database_for_eys_gene,\n", " parse_lovd,\n", + " parse_gnomad,\n", " LOVD_PATH,\n", - " set_lovd_dtypes)\n", + " set_lovd_dtypes,\n", + " set_gnomad_dtypes,\n", + " request_gnomad_api_data,\n", + " merge_gnomad_lovd,\n", + " GNOMAD_PATH,\n", + " )\n", "from api.data import save_lovd_as_vcf\n", + "\n", + "\n", "pd.options.display.max_columns = 0" - ] + ], + "outputs": [], + "execution_count": null }, { "cell_type": "code", - "execution_count": 10, "id": "f49f7691a27aa7b4", "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-08-11T16:16:57.305309Z", - "start_time": "2024-08-11T16:16:56.668571Z" - } + "collapsed": false }, - "outputs": [], "source": [ "store_database_for_eys_gene(\"lovd\", override=False)" - ] + ], + "outputs": [], + "execution_count": null }, { "cell_type": "code", - "execution_count": 2, "id": "cf5c45c0f7b9de0f", "metadata": { - "ExecuteTime": { - "end_time": "2024-05-13T15:38:24.591752Z", - "start_time": "2024-05-13T15:38:19.498594Z" - }, - "collapsed": false + "collapsed": false, + "jupyter": { + "outputs_hidden": false + } }, - "outputs": [], "source": [ "data = parse_lovd(LOVD_PATH + \"/lovd_data.txt\")" - ] + ], + "outputs": [], + "execution_count": null }, { + "metadata": {}, "cell_type": "code", - "execution_count": 8, - "id": "8a089e29bfc8c119", - "metadata": { - "ExecuteTime": { - "end_time": "2024-05-13T15:12:07.510712Z", - "start_time": "2024-05-13T15:12:07.366319Z" - } - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Genes\n" - ] - }, - { - "data": { - "text/html": [ - "
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012PSORSpsoriasis, pustular, generalized (PSORS)<NA>62012-07-06 21:50:3262019-08-12 13:38:21
158CORDdystrophy, cone-rod (CORD)<NA>62012-09-22 11:31:2562020-08-30 09:43:59
2112RPretinitis pigmentosa (RP)26800012013-02-21 17:12:3662021-01-18 09:53:26
3139IDintellectual disability (ID)<NA>842013-06-04 18:18:0762015-02-09 10:02:49
4173SLOSSmith-Lemli-Opitz syndrome (SLOS)AR27040062013-08-01 11:16:1462021-12-10 21:51:32
5198?unclassified / mixed<NA>62013-09-13 14:21:4762016-10-22 17:54:40
62156-retinitis pigmentosa, X-linked, and sinorespir...30045562014-09-25 23:29:4062021-12-10 21:51:32
72440RP25retinitis pigmentosa, type 25 (RP25)AR60277262014-09-25 23:29:4062021-12-10 21:51:32
84211RParretinitis pigmentosa, autosomal recessive (RPar)<NA>62015-02-27 18:58:57<NA>NaT
94214-retinal disease<NA>62015-02-27 19:48:0712023-03-09 14:26:26
104249macular dystrophydystrophy, macular<NA>62015-05-04 22:10:5862024-02-15 21:18:39
115086HLhearing loss (HL)<NA>62015-10-23 11:41:0562015-10-23 11:43:00
125415USHUsher syndrome (USH)<NA>62018-04-02 16:40:44<NA>NaT
135468uveitisuveitis<NA>62018-08-22 09:47:04<NA>NaT
146906DEEencephalopathy, developmental and epileptic<NA>62022-04-07 09:24:23<NA>NaT
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iddiseaseidindividualidowned_byPhenotype/InheritancePhenotype/AgePhenotype/AdditionalPhenotype/Biochem_paramPhenotype/Age/OnsetPhenotype/Age/DiagnosisPhenotype/Severity_scorePhenotype/OnsetPhenotype/ProteinPhenotype/Tumor/MSIPhenotype/Enzyme/CPKPhenotype/Heart/MyocardiumPhenotype/LungPhenotype/Diagnosis/DefinitePhenotype/Diagnosis/InitialPhenotype/Diagnosis/Criteria
08121356Familial, autosomal recessive
1265821039Familial, autosomal recessive
2941173196225Familial2-3 toe syndactyly5
326525421433096229Unknownretinitis pigmentosa
426538421433109229Unknownretinitis pigmentosa
...............................................................
12663369011984477026Unknownretinitis pigmentosa, simplex
12673369061984477076Unknownretinitis pigmentosa, simplex
12683369151984477166Unknownretinitis pigmentosa, simplex
12693369171984477186Unknownretinitis pigmentosa, simplex
12703369191984477206Unknownretinitis pigmentosa, simplex
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01261351662012-07-07 19:04:1962012-07-07 19:12:08RT-PCR;SEQDNA;RNA
121121013962012-09-22 11:36:24<NA>NaTSEQDNA
21640196212562010-03-11 16:36:41252012-04-13 15:18:00SEQDNA
3165571660515525522014-05-23 13:12:43<NA>NaTSEQ-NG-IDNA
4331643309612292292012-02-04 15:20:0162012-05-18 13:59:33SEQ;SEQ-NG-SDNA
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14454492794477021662024-01-26 10:23:59<NA>NaTSEQ-NGDNAWGS
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idalleleeffectidchromosomeposition_g_startposition_g_endtypeaverage_frequencyowned_byVariantOnGenome/DBIDVariantOnGenome/DNAVariantOnGenome/FrequencyVariantOnGenome/ReferenceVariantOnGenome/Restriction_siteVariantOnGenome/Published_asVariantOnGenome/RemarksVariantOnGenome/Genetic_originVariantOnGenome/SegregationVariantOnGenome/dbSNPVariantOnGenome/VIPVariantOnGenome/MethylationVariantOnGenome/ISCNVariantOnGenome/DNA/hg38VariantOnGenome/ClinVarVariantOnGenome/ClinicalClassificationVariantOnGenome/ClinicalClassification/Method
03642635066449897164498971subst0.000743552EYS_000007g.64498971A>GGermline0g.63789078A>GVUS
15988135566565575865655758subst0.001153229EYS_000001g.65655758T>GExAC: 60, 19750, 0, 0.003038{PMID:Neveling 2012:22334370}Q770PGermlineyes0g.64945865T>GVUS
25988311166533614365336143subst0.224189229EYS_000002g.65336143G>AExAC: 3936, 19366, 441, 0.2032{PMID:Neveling 2012:22334370}p.?unaffected brother also this variant homozygousGermlineno0g.64626250G>Abenign
35988411566530086965300869subst0.000838229EYS_000003g.65300869G>AExAC: 12, 19406, 0, 0.0006184{PMID:Neveling 2012:22334370}(P1631S)predicted benign, disease-related variant in o...Germline0g.64590976G>Abenign
45988511166501699865016999del0.000000229EYS_000004g.65016998_65016999delExAC: 9866, 18292, 921, 0.5394{PMID:Neveling 2012:22334370}6045-4_6045-3delpredicted benignGermlineyes0g.64307105_64307106delbenign
.................................................................................
253696421103066576763465767634subst0.2430222330EYS_000248g.65767634G>AEYS(NM_001292009.2):c.2024-15_2024-14delTCinsTTVKGL data sharing initiative NederlandCLASSIFICATION recordlikely benign
253796421203066576764365767643del0.0000002330EYS_000926g.65767643delEYS(NM_001292009.2):c.2024-15delTVKGL data sharing initiative NederlandCLASSIFICATION recordlikely benign
253896421505066600592766005927subst0.0001122327EYS_000253g.66005927C>TEYS(NM_001142800.1):c.1852G>A (p.G618S), EYS(N...VKGL data sharing initiative NederlandCLASSIFICATION recordVUS
253996421605066604487466044874subst0.0000822327EYS_000256g.66044874T>CEYS(NM_001292009.2):c.1765A>G (p.R589G)VKGL data sharing initiative NederlandCLASSIFICATION recordVUS
254097731409066443094364430943subst0.0000071804EYS_000060g.64430943A>TEYS(NM_001142800.2):c.8984T>A (p.(Ile2995Asn))...VKGL data sharing initiative NederlandCLASSIFICATION recordpathogenic
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idtranscriptideffectidposition_c_startposition_c_start_intronposition_c_endposition_c_end_intronVariantOnTranscript/DNAVariantOnTranscript/RNAVariantOnTranscript/ProteinVariantOnTranscript/Exon
0364267329507558075580c.7558T>Cr.(?)p.(Phe2520Leu)38
1598817329552309023090c.2309A>Cr.(?)p.(Gln770Pro)15
2598837329113444-53444-5c.3444-5C>Tr.(?)p.(=)22i
3598847329154891048910c.4891C>Tr.(?)p.(Pro1631Ser)26
4598857329116079-46079-3c.6079-4_6079-3delr.(?)p.(=)29i
....................................
25369642117329302024-142024-14c.2024-14C>Tr.(=)p.(=)
25379642127329302024-152024-15c.2024-15delr.(=)p.(=)
25389642157329501852018520c.1852G>Ar.(?)p.(Gly618Ser)
25399642167329501765017650c.1765A>Gr.(?)p.(Arg589Gly)
25409773147329908984089840c.8984T>Ar.(?)p.(Ile2995Asn)
\n", - "

2541 rows × 11 columns

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" - ], - "text/plain": [ - " id transcriptid ... VariantOnTranscript/Protein VariantOnTranscript/Exon\n", - "0 36426 7329 ... p.(Phe2520Leu) 38\n", - "1 59881 7329 ... p.(Gln770Pro) 15\n", - "2 59883 7329 ... p.(=) 22i\n", - "3 59884 7329 ... p.(Pro1631Ser) 26\n", - "4 59885 7329 ... p.(=) 29i\n", - "... ... ... ... ... ...\n", - "2536 964211 7329 ... p.(=) \n", - "2537 964212 7329 ... p.(=) \n", - "2538 964215 7329 ... p.(Gly618Ser) \n", - "2539 964216 7329 ... p.(Arg589Gly) \n", - "2540 977314 7329 ... p.(Ile2995Asn) \n", - "\n", - "[2541 rows x 11 columns]" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Screenings_To_Variants\n" - ] - }, - { - "data": { - "text/html": [ - "
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screeningidvariantid
0126783293
1211790459
21640235838
31655736426
43316459884
.........
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2149 rows × 2 columns

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" - ], - "text/plain": [ - " screeningid variantid\n", - "0 126 783293\n", - "1 211 790459\n", - "2 1640 235838\n", - "3 16557 36426\n", - "4 33164 59884\n", - "... ... ...\n", - "2144 449279 959046\n", - "2145 449284 959051\n", - "2146 449293 959060\n", - "2147 449295 959474\n", - "2148 449297 959064\n", - "\n", - "[2149 rows x 2 columns]" - ] - }, - "metadata": {}, - "output_type": "display_data" - } + "source": [ + "gnomad_data = request_gnomad_api_data(\"EYS\")\n", + "\n", + "display(gnomad_data)" + ], + "id": "64482c033c794fb4", + "outputs": [], + "execution_count": null + }, + { + "metadata": {}, + "cell_type": "code", + "source": [ + "store_database_for_eys_gene('gnomad', False)\n", + "\n", + "gnomad_data_2 = parse_gnomad(GNOMAD_PATH +'/gnomad_data.csv')" + ], + "id": "60f3f3074a9b19f4", + "outputs": [], + "execution_count": null + }, + { + "metadata": {}, + "cell_type": "code", + "source": "display(gnomad_data_2)", + "id": "9d3e4d6b5f7be127", + "outputs": [], + "execution_count": null + }, + { + "metadata": {}, + "cell_type": "code", + "source": [ + "gnomad_data_2.to_csv('C:\\\\Users\\\\Kajus\\\\Desktop\\\\gnomad_data_downloaded.csv', index=False)\n", + "gnomad_data.to_csv('C:\\\\Users\\\\Kajus\\\\Desktop\\\\gnomad_data_api.csv', index=False)" + ], + "id": "2e869f5c77dbe3d3", + "outputs": [], + "execution_count": null + }, + { + "metadata": {}, + "cell_type": "code", + "source": [ + "len(gnomad_data_2), len(gnomad_data)\n", + "\n", + "print(len(gnomad_data_2) - len(gnomad_data))" + ], + "id": "9efafb201061c146", + "outputs": [], + "execution_count": null + }, + { + "metadata": {}, + "cell_type": "code", + "source": "gnomad_data", + "id": "96283480cccf641", + "outputs": [], + "execution_count": null + }, + { + "metadata": {}, + "cell_type": "code", + "source": [ + "missing_from_api = []\n", + "\n", + "for i in gnomad_data['gnomAD ID']:\n", + " if(i in gnomad_data_2['gnomAD ID'].values):\n", + " continue\n", + " missing_from_api.append(i)\n", + "\n", + "len(missing_from_api)\n", + "\n", + "missing_data = gnomad_data.loc[gnomad_data['gnomAD ID'].isin(missing_from_api)]\n", + "\n", + "missing_data" + ], + "id": "d0eb0a6db96d31c8", + "outputs": [], + "execution_count": null + }, + { + "metadata": {}, + "cell_type": "code", + "source": "missing_data.to_csv('C:\\\\Users\\\\Kajus\\\\Desktop\\\\gnomad_data_missing.csv', index=False)", + "id": "388120b03b094511", + "outputs": [], + "execution_count": null + }, + { + "metadata": {}, + "cell_type": "code", + "source": [ + "set_lovd_dtypes(data)\n", + "set_gnomad_dtypes(gnomad_data)\n", + "\n", + "variants_on_genome = data[\"Variants_On_Genome\"].copy()\n", + "\n", + "lovd_data = pd.merge(data[\"Variants_On_Transcripts\"],\n", + " variants_on_genome[['id','VariantOnGenome/DNA/hg38']],\n", + " on='id',\n", + " how='left')\n", + "\n", + "gnomad_data = gnomad_data.copy()\n", + "final_data = merge_gnomad_lovd(lovd_data, gnomad_data)\n", + "final_data" ], + "id": "96453d88e353aeb1", + "outputs": [], + "execution_count": null + }, + { + "metadata": {}, + "cell_type": "code", "source": [ "for i in data:\n", " print(i)\n", " display(data[i])" - ] + ], + "id": "8a089e29bfc8c119", + "outputs": [], + "execution_count": null }, { + "metadata": {}, "cell_type": "code", - "execution_count": null, - "id": "ef07740b2fa63e42", - "metadata": { - "collapsed": false - }, - "outputs": [], "source": [ "set_lovd_dtypes(data)\n", "for i in data:\n", " print(i)\n", " display(data[i].info())" - ] + ], + "id": "ef07740b2fa63e42", + "outputs": [], + "execution_count": null }, { + "metadata": {}, "cell_type": "code", - "execution_count": 3, + "source": "save_lovd_as_vcf(data[\"Variants_On_Genome\"], \"./lovd.vcf\")", "id": "c968af1617be40db", - "metadata": { - "ExecuteTime": { - "end_time": "2024-05-13T15:38:25.149624Z", - "start_time": "2024-05-13T15:38:24.807199Z" - } - }, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "WARNING:root:Skipping variant g.64307105_64307106del\n", - "WARNING:root:Skipping variant g.65495379dup\n", - "WARNING:root:Skipping variant g.65495379dup\n", - "WARNING:root:Skipping variant \n", - 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"WARNING:root:Skipping variant g.64591505_64591506delinsCT\n", - "WARNING:root:Skipping variant g.65495005_65495008delinsAAG\n", - "WARNING:root:Skipping variant g.65495005_65495008delinsAAG\n", - "WARNING:root:Skipping variant g.65384480dup\n", - "WARNING:root:Skipping variant g.63726599_63726600del\n", - "WARNING:root:Skipping variant g.65495005_65495008delinsAAG\n", - "WARNING:root:Skipping variant g.65495005_65495008delinsAAG\n", - "WARNING:root:Skipping variant g.65495005_65495008delinsAAG\n", - "WARNING:root:Skipping variant g.63726599_63726600del\n", - "WARNING:root:Skipping variant g.65495005_65495008delinsAAG\n", - "WARNING:root:Skipping variant g.63726599_63726600del\n", - "WARNING:root:Skipping variant g.65335102del\n", - "WARNING:root:Skipping variant g.65335102del\n", - "WARNING:root:Skipping variant g.65335102del\n", - "WARNING:root:Skipping variant g.64591514_64591520del\n", - "WARNING:root:Skipping variant g.63721377_63721384del\n", - "WARNING:root:Skipping variant g.64591514_64591520del\n", - "WARNING:root:Skipping variant g.63721377_63721384del\n", - "WARNING:root:Skipping variant g.64591514_64591520del\n", - "WARNING:root:Skipping variant g.64591514_64591520del\n", - "WARNING:root:Skipping variant g.64591514_64591520del\n", - "WARNING:root:Skipping variant g.63999116del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.64066349del\n", - "WARNING:root:Skipping variant g.63999110_63999111del\n", - "WARNING:root:Skipping variant g.63999110_63999111del\n", - "WARNING:root:Skipping variant g.65321830_65370656del\n", - "WARNING:root:Skipping variant g.63720850_63720853del\n", - "WARNING:root:Skipping variant g.65321830_65370656del\n", - "WARNING:root:Skipping variant g.63720850_63720853del\n", - "WARNING:root:Skipping variant g.65321830_65370656del\n", - "WARNING:root:Skipping variant g.63720850_63720853del\n", - "WARNING:root:Skipping variant g.64066349del\n", - "WARNING:root:Skipping variant g.63806240del\n", - "WARNING:root:Skipping variant g.63806240del\n", - "WARNING:root:Skipping variant g.65495332_65495333dup\n", - "WARNING:root:Skipping variant g.65324960_65416038del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.65295915del\n", - "WARNING:root:Skipping variant g.65494988_65495003del\n", - "WARNING:root:Skipping variant g.65494988_65495003del\n", - "WARNING:root:Skipping variant g.65494988_65495003del\n", - "WARNING:root:Skipping variant g.65494988_65495003del\n", - "WARNING:root:Skipping variant g.65494988_65495003del\n", - "WARNING:root:Skipping variant g.65494988_65495003del\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.65384480dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.65344144_65344152delinsCTTTTCG\n", - "WARNING:root:Skipping variant g.63984409_63984410delinsACGAT\n", - "WARNING:root:Skipping variant g.63788163_63788164del\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64912603dup\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590700dup\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.64590700dup\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64066349del\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64591845del\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.63984390del\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.63721651_63721652insCA\n", - "WARNING:root:Skipping variant g.64590665_64590666del\n", - "WARNING:root:Skipping variant g.63721651_63721652insCA\n", - "WARNING:root:Skipping variant g.64590665_64590666del\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64591466dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64591480del\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.63788136del\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.63720730_63720733del\n", - "WARNING:root:Skipping variant g.64591514_64591520del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.64591514_64591520del\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64912603dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590665_64590666del\n", - "WARNING:root:Skipping variant g.63721652_63721655dup\n", - "WARNING:root:Skipping variant g.64590665_64590666del\n", - "WARNING:root:Skipping variant g.63721652_63721655dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64912603dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64591313del\n", - "WARNING:root:Skipping variant g.64439355_64439356insA\n", - "WARNING:root:Skipping variant g.63984543_63984570del\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.63984537_63984542dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64614795_64939832del\n", - "WARNING:root:Skipping variant g.64614795_64939832del\n", - "WARNING:root:Skipping variant g.64614795_64939832del\n", - "WARNING:root:Skipping variant g.63721576del\n", - "WARNING:root:Skipping variant g.64902132_64902133del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.63720889dup\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.65495379dup\n", - "WARNING:root:Skipping variant g.64066349del\n", - "WARNING:root:Skipping variant g.65495379dup\n", - "WARNING:root:Skipping variant g.64591514_64591520del\n", - "WARNING:root:Skipping variant g.63721625dup\n", - "WARNING:root:Skipping variant g.65405300dup\n", - "WARNING:root:Skipping variant g.64813506del\n", - "WARNING:root:Skipping variant g.64591514_64591520del\n", - "WARNING:root:Skipping variant g.63720753_63720754dup\n", - "WARNING:root:Skipping variant g.65405325dup\n", - "WARNING:root:Skipping variant g.65405325dup\n", - "WARNING:root:Skipping variant g.65405325dup\n", - "WARNING:root:Skipping variant g.65405325dup\n", - "WARNING:root:Skipping variant g.65405325dup\n", - "WARNING:root:Skipping variant g.65405325dup\n", - "WARNING:root:Skipping variant g.65405325dup\n", - "WARNING:root:Skipping variant g.65405325dup\n", - "WARNING:root:Skipping variant g.65405325dup\n", - "WARNING:root:Skipping variant g.65405325dup\n", - "WARNING:root:Skipping variant g.65405325dup\n", - "WARNING:root:Skipping variant g.65405325dup\n", - "WARNING:root:Skipping variant g.64591514_64591520del\n", - "WARNING:root:Skipping variant g.65707136_65707226del\n", - "WARNING:root:Skipping variant g.65495348del\n", - "WARNING:root:Skipping variant g.64591514_64591520del\n", - "WARNING:root:Skipping variant g.64591514_64591520del\n", - "WARNING:root:Skipping variant g.63720845_63720846del\n", - "WARNING:root:Skipping variant g.63726607del\n", - "WARNING:root:Skipping variant g.63721786dup\n", - "WARNING:root:Skipping variant g.63721640del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.65344138dup\n", - "WARNING:root:Skipping variant g.65402503del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.64590699_64590700del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.64590699_64590700del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.65384384_65384387del\n", - "WARNING:root:Skipping variant g.64066349del\n", - "WARNING:root:Skipping variant g.65384480dup\n", - "WARNING:root:Skipping variant g.63806228dup\n", - "WARNING:root:Skipping variant g.63999116del\n", - "WARNING:root:Skipping variant g.64591514_64591520del\n", - "WARNING:root:Skipping variant g.64066349del\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.65384384_65384387del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.63721377_63721384del\n", - "WARNING:root:Skipping variant g.63999110_63999111del\n", - "WARNING:root:Skipping variant g.63999110_63999111del\n", - "WARNING:root:Skipping variant g.63999110_63999111del\n", - "WARNING:root:Skipping variant g.64066349del\n", - "WARNING:root:Skipping variant g.64591514_64591520del\n", - "WARNING:root:Skipping variant g.64439331del\n", - "WARNING:root:Skipping variant g.64066349del\n", - "WARNING:root:Skipping variant g.65494957dup\n", - "WARNING:root:Skipping variant g.63720995del\n", - "WARNING:root:Skipping variant g.64591514_64591520del\n", - "WARNING:root:Skipping variant g.63721771_63721776del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.64591514_64591520del\n", - "WARNING:root:Skipping variant g.65494957dup\n", - "WARNING:root:Skipping variant g.64591977del\n", - "WARNING:root:Skipping variant g.64886728_64886736del\n", - "WARNING:root:Skipping variant g.65495379dup\n", - "WARNING:root:Skipping variant g.63721138del\n", - "WARNING:root:Skipping variant g.65353541del\n", - "WARNING:root:Skipping variant g.65353541del\n", - "WARNING:root:Skipping variant g.65494988_65495002del\n", - "WARNING:root:Skipping variant g.65494988_65495002del\n", - "WARNING:root:Skipping variant g.65494988_65495002del\n", - "WARNING:root:Skipping variant g.65494988_65495002del\n", - "WARNING:root:Skipping variant g.65494988_65495002del\n", - "WARNING:root:Skipping variant g.65494988_65495002del\n", - "WARNING:root:Skipping variant g.65494988_65495002del\n", - "WARNING:root:Skipping variant g.65494988_65495002del\n", - "WARNING:root:Skipping variant g.65494988_65495002del\n", - "WARNING:root:Skipping variant g.65494988_65495002del\n", - "WARNING:root:Skipping variant g.65295857dup\n", - "WARNING:root:Skipping variant g.65295856_65295857dup\n", - "WARNING:root:Skipping variant g.64591514_64591520del\n", - "WARNING:root:Skipping variant g.64307105_64307106del\n", - "WARNING:root:Skipping variant g.64307103_64307106del\n", - "WARNING:root:Skipping variant g.63726618_63726622del\n", - "WARNING:root:Skipping variant g.63720642_63720644del\n", - "WARNING:root:Skipping variant g.65295857dup\n", - "WARNING:root:Skipping variant g.64307105_64307106del\n", - "WARNING:root:Skipping variant g.65353541del\n", - "WARNING:root:Skipping variant g.64591918_64591919del\n", - "WARNING:root:Skipping variant g.64591514_64591520del\n", - "WARNING:root:Skipping variant g.64590525_64590548del\n", - "WARNING:root:Skipping variant g.64388841_64388843del\n", - "WARNING:root:Skipping variant g.64307084_64307085del\n", - "WARNING:root:Skipping variant g.64307105_64307106del\n", - "WARNING:root:Skipping variant g.64307103_64307106del\n", - "WARNING:root:Skipping variant g.64307105_64307106del\n", - "WARNING:root:Skipping variant g.64593097_64593101del\n", - "WARNING:root:Skipping variant g.65384384_65384387del\n", - "WARNING:root:Skipping variant g.63999110_63999111del\n", - "WARNING:root:Skipping variant g.64066349del\n", - "WARNING:root:Skipping variant g.64439213del\n", - "WARNING:root:Skipping variant g.63721771_63721776del\n", - "WARNING:root:Skipping variant g.65494957dup\n", - "WARNING:root:Skipping variant g.65494988_65495008delinsAAAAG\n", - "WARNING:root:Skipping variant g.63720799_63720808del\n", - "WARNING:root:Skipping variant g.63726584del\n", - "WARNING:root:Skipping variant g.63726599_63726600del\n", - "WARNING:root:Skipping variant g.63726648del\n", - "WARNING:root:Skipping variant g.64349976_64426764del\n", - "WARNING:root:Skipping variant g.64591505_64591506delinsCT\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.63720728_63720729del\n", - "WARNING:root:Skipping variant g.63720845_63720846del\n", - "WARNING:root:Skipping variant g.63721162del\n", - "WARNING:root:Skipping variant g.63721237_63721240del\n", - "WARNING:root:Skipping variant g.63721343del\n", - "WARNING:root:Skipping variant g.63721730_63721733del\n", - "WARNING:root:Skipping variant g.63721763_63721767del\n", - "WARNING:root:Skipping variant g.63721787dup\n", - "WARNING:root:Skipping variant g.63726618_63726622del\n", - "WARNING:root:Skipping variant g.63788163_63788164del\n", - "WARNING:root:Skipping variant g.63984389del\n", - "WARNING:root:Skipping variant g.64066348del\n", - "WARNING:root:Skipping variant g.64590909dup\n", - "WARNING:root:Skipping variant g.64591309del\n", - "WARNING:root:Skipping variant g.64591858_64591859del\n", - "WARNING:root:Skipping variant g.64886728_64886736del\n", - "WARNING:root:Skipping variant g.64945814del\n", - "WARNING:root:Skipping variant g.65344143_65344144insCTTT\n", - "WARNING:root:Skipping variant g.65344146_65344151del\n", - "WARNING:root:Skipping variant g.65344181dup\n", - "WARNING:root:Skipping variant g.65384473dup\n", - "WARNING:root:Skipping variant g.65405287del\n", - "WARNING:root:Skipping variant g.65494885_65494887del\n", - "WARNING:root:Skipping variant g.65494961del\n", - "WARNING:root:Skipping variant g.65495205del\n", - "WARNING:root:Skipping variant g.65495296_65495297del\n", - "WARNING:root:Skipping variant g.64590909dup\n", - "WARNING:root:Skipping variant g.65384473dup\n", - "WARNING:root:Skipping variant g.65405287del\n", - "WARNING:root:Skipping variant g.65494885_65494887del\n", - "WARNING:root:Skipping variant g.63762589del\n", - "WARNING:root:Skipping variant g.63720874del\n", - "WARNING:root:Skipping variant g.63721619_63721620insGT\n", - "WARNING:root:Skipping variant g.63788268dup\n", - "WARNING:root:Skipping variant g.63984369_63984392del\n", - "WARNING:root:Skipping variant g.65057740_65057741insA\n", - "WARNING:root:Skipping variant g.65057740_65057741insAA\n", - "WARNING:root:Skipping variant g.65057750dup\n", - "WARNING:root:Skipping variant g.65384384_65384387del\n", - "WARNING:root:Skipping variant g.65402624dup\n", - "WARNING:root:Skipping variant g.65405377dup\n", - "WARNING:root:Skipping variant g.65494957dup\n", - "WARNING:root:Skipping variant g.65494957dup\n", - "WARNING:root:Skipping variant g.65495379dup\n", - "WARNING:root:Skipping variant g.63721625dup\n", - "WARNING:root:Skipping variant g.63721704dup\n", - "WARNING:root:Skipping variant g.65353537dup\n", - "WARNING:root:Skipping variant g.65335105_65335108del\n", - "WARNING:root:Skipping variant g.63721385_63721386del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - 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"WARNING:root:Skipping variant g.63720737_63720746del\n", - "WARNING:root:Skipping variant g.63720737_63720746del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.63765706_63791377del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.63781919_63803805del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.64892926_64948294del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64591845del\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.64945857dup\n", - "WARNING:root:Skipping variant g.63721377_63721384del\n", - "WARNING:root:Skipping variant g.63721377_63721384del\n", - "WARNING:root:Skipping variant g.63721377_63721384del\n", - "WARNING:root:Skipping variant g.63721377_63721384del\n", - "WARNING:root:Skipping variant g.63721557_63721558insA\n", - "WARNING:root:Skipping variant g.64439319_64439323del\n", - "WARNING:root:Skipping variant g.65296021del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.65495181del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.65384425del\n", - "WARNING:root:Skipping variant g.64591039_64591042del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.63721599_63721604del\n", - "WARNING:root:Skipping variant g.64902132_64902133del\n", - "WARNING:root:Skipping variant g.65494988_65495008delinsAAAAG\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.65495236del\n", - "WARNING:root:Skipping variant g.64590908_64590909insT\n", - "WARNING:root:Skipping variant g.64617409_64617411dup\n", - "WARNING:root:Skipping variant g.65295857dup\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.64066349del\n", - "WARNING:root:Skipping variant g.64066349del\n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant g.63720845_63720846del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.63720668dup\n", - "WARNING:root:Skipping variant g.(63741975_63762461)_(63778180_63788105)dup\n", - "WARNING:root:Skipping variant g.65296051_65296052del\n", - "WARNING:root:Skipping variant g.65296051_65296052del\n", - "WARNING:root:Skipping variant g.64439200dup\n", - "WARNING:root:Skipping variant g.63720737_63720746del\n", - "WARNING:root:Skipping variant g.63720737_63720746del\n", - "WARNING:root:Skipping variant g.65494885_65494887del\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant g.64590911dup\n", - "WARNING:root:Skipping variant \n", - "WARNING:root:Skipping variant \n", - 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You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.\n", - "2024-05-13 18:58:41.794769: I external/local_tsl/tsl/cuda/cudart_stub.cc:32] Could not find cuda drivers on your machine, GPU will not be used.\n", - "2024-05-13 18:58:41.797917: I external/local_tsl/tsl/cuda/cudart_stub.cc:32] Could not find cuda drivers on your machine, GPU will not be used.\n", - "2024-05-13 18:58:41.857361: I tensorflow/core/platform/cpu_feature_guard.cc:210] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.\n", - "To enable the following instructions: AVX2 AVX_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.\n", - "2024-05-13 18:58:42.410244: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT\n", - "2024-05-13 18:58:42.957291: I external/local_xla/xla/stream_executor/cuda/cuda_executor.cc:998] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero. See more at https://github.com/torvalds/linux/blob/v6.0/Documentation/ABI/testing/sysfs-bus-pci#L344-L355\n", - "2024-05-13 18:58:42.957684: W tensorflow/core/common_runtime/gpu/gpu_device.cc:2251] Cannot dlopen some GPU libraries. Please make sure the missing libraries mentioned above are installed properly if you would like to use GPU. Follow the guide at https://www.tensorflow.org/install/gpu for how to download and setup the required libraries for your platform.\n", - "Skipping registering GPU devices...\n", - "WARNING:absl:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.\n", - "WARNING:absl:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.\n", - "WARNING:absl:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.\n", - "WARNING:absl:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.\n", - "WARNING:absl:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\u001B[1m1/1\u001B[0m \u001B[32m━━━━━━━━━━━━━━━━━━━━\u001B[0m\u001B[37m\u001B[0m \u001B[1m1s\u001B[0m 595ms/step\n", - "\u001B[1m1/1\u001B[0m \u001B[32m━━━━━━━━━━━━━━━━━━━━\u001B[0m\u001B[37m\u001B[0m \u001B[1m1s\u001B[0m 554ms/step\n", - "\u001B[1m1/1\u001B[0m \u001B[32m━━━━━━━━━━━━━━━━━━━━\u001B[0m\u001B[37m\u001B[0m \u001B[1m1s\u001B[0m 553ms/step\n", - "\u001B[1m1/1\u001B[0m \u001B[32m━━━━━━━━━━━━━━━━━━━━\u001B[0m\u001B[37m\u001B[0m \u001B[1m1s\u001B[0m 548ms/step\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "WARNING:tensorflow:5 out of the last 5 calls to .one_step_on_data_distributed at 0x7dee981abf40> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has reduce_retracing=True option that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for more details.\n", - "WARNING:tensorflow:5 out of the last 5 calls to .one_step_on_data_distributed at 0x7dee981abf40> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has reduce_retracing=True option that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for more details.\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\u001B[1m1/1\u001B[0m \u001B[32m━━━━━━━━━━━━━━━━━━━━\u001B[0m\u001B[37m\u001B[0m \u001B[1m1s\u001B[0m 548ms/step\n", - "\u001B[1m1/1\u001B[0m \u001B[32m━━━━━━━━━━━━━━━━━━━━\u001B[0m\u001B[37m\u001B[0m \u001B[1m0s\u001B[0m 49ms/step\n", - "\u001B[1m1/1\u001B[0m \u001B[32m━━━━━━━━━━━━━━━━━━━━\u001B[0m\u001B[37m\u001B[0m \u001B[1m0s\u001B[0m 51ms/step\n", - "\u001B[1m1/1\u001B[0m \u001B[32m━━━━━━━━━━━━━━━━━━━━\u001B[0m\u001B[37m\u001B[0m \u001B[1m0s\u001B[0m 51ms/step\n", - "\u001B[1m1/1\u001B[0m \u001B[32m━━━━━━━━━━━━━━━━━━━━\u001B[0m\u001B[37m\u001B[0m \u001B[1m0s\u001B[0m 59ms/step\n", - "\u001B[1m1/1\u001B[0m \u001B[32m━━━━━━━━━━━━━━━━━━━━\u001B[0m\u001B[37m\u001B[0m \u001B[1m0s\u001B[0m 53ms/step\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "WARNING:root:dede['G|EYS|0.00|0.00|0.00|0.00|3|9|-20|9']\n" - ] - }, - { - "data": { - "text/plain": [ - "0" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ "from subprocess import Popen\n", "\n", - "\n", "process = Popen(\"spliceai -I ./lovd.vcf -O ./lovd_output.vcf -R ../tools/spliceai/hg38.fa -A grch38\".split())\n", "process.wait()" - ] + ], + "id": "c7ff16903e0c52bd", + "outputs": [], + "execution_count": null }, { - "cell_type": "code", - "execution_count": 1, - "id": "0514ccc3-5c91-41ad-ab15-f4158030ea14", "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/home/nojsaj/kath/tools/revel/revel.py:9: DtypeWarning: Columns (0,2) have mixed types. Specify dtype option on import or set low_memory=False.\n", - " revel_data = pd.read_csv(revel_file)\n" - ] - }, - { - "data": { - "text/html": [ - "
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2875612966565575864945865TGQP0.344ENST00000503581;ENST00000370621;ENST00000370616
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" - ], - "text/plain": [ - " chr hg19_pos grch38_pos ref alt aaref aaalt REVEL \\\n", - "28756127 6 65655758 64945865 T A Q L 0.188 \n", - "28756128 6 65655758 64945865 T C Q R 0.111 \n", - "28756129 6 65655758 64945865 T G Q P 0.344 \n", - "\n", - " Ensembl_transcriptid \n", - "28756127 ENST00000503581;ENST00000370621;ENST00000370616 \n", - "28756128 ENST00000503581;ENST00000370621;ENST00000370616 \n", - "28756129 ENST00000503581;ENST00000370621;ENST00000370616 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], + "cell_type": "code", "source": [ - "from tools import get_revel_scores\n", + "from api.tools import get_revel_scores\n", "\n", "chromosome = 6\n", "position = 65655758\n", @@ -3905,86 +230,26 @@ "results = get_revel_scores(chromosome, position)\n", "\n", "display(results)" - ] - }, - { - "cell_type": "code", - "outputs": [], - "source": [ - "from api.data.collection import store_database_for_eys_gene\n", - "store_database_for_eys_gene(\"clinvar\", override=False)" ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-08-12T16:46:07.973915Z", - "start_time": "2024-08-12T16:46:07.970874Z" - } - }, - "id": "b80a1049abe7596e", - "execution_count": 12 + "id": "0514ccc3-5c91-41ad-ab15-f4158030ea14", + "outputs": [], + "execution_count": null }, { + "metadata": {}, "cell_type": "code", - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "The file at ../data/lovd/lovd_data.txt already exists.\n" - ] - } - ], - "source": [ - "from api.data.collection import store_database_for_eys_gene\n", - "store_database_for_eys_gene(\"lovd\", override=False)" - ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-08-12T16:47:56.094297Z", - "start_time": "2024-08-12T16:47:56.090300Z" - } - }, - "id": "a1e10fc8175753a0", - "execution_count": 4 + "source": "", + "id": "6f0abfb50bd211a0", + "outputs": [], + "execution_count": null }, { - "cell_type": "code", - "outputs": [ - { - "data": { - "text/plain": " gnomAD ID Chromosome Position rsIDs Reference \\\n0 6-63720525-A-G 6 63720525 rs1768331164 A \n1 6-63720525-A-T 6 63720525 rs1768331164 A \n2 6-63720526-T-A 6 63720526 T \n3 6-63720531-C-CAA 6 63720531 C \n4 6-63720531-C-G 6 63720531 rs927390284 C \n... ... ... ... ... ... \n11083 6-65495478-G-A 6 65495478 rs530118054 G \n11084 6-65495479-G-A 6 65495479 rs1766225632 G \n11085 6-65495482-A-G 6 65495482 rs1766225707 A \n11086 6-65495484-T-G 6 65495484 rs1766225807 T \n11087 6-65495485-T-C 6 65495485 T \n\n Alternate Source Filters - exomes \\\n0 G gnomAD Exomes,gnomAD Genomes PASS \n1 T gnomAD Genomes \n2 A gnomAD Exomes PASS \n3 CAA gnomAD Exomes PASS \n4 G gnomAD Exomes,gnomAD Genomes PASS \n... ... ... ... \n11083 A gnomAD Exomes,gnomAD Genomes PASS \n11084 A gnomAD Exomes PASS \n11085 G gnomAD Exomes,gnomAD Genomes PASS \n11086 G gnomAD Exomes PASS \n11087 C gnomAD Exomes PASS \n\n Filters - genomes Transcript ... Homozygote Count Amish \\\n0 PASS ENST00000503581.6 ... 0 \n1 PASS ENST00000503581.6 ... 0 \n2 ENST00000503581.6 ... 0 \n3 ENST00000503581.6 ... 0 \n4 PASS ENST00000503581.6 ... 0 \n... ... ... ... ... \n11083 PASS ENST00000503581.6 ... 0 \n11084 ENST00000503581.6 ... 0 \n11085 PASS ENST00000503581.6 ... 0 \n11086 ENST00000503581.6 ... 0 \n11087 ENST00000503581.6 ... 0 \n\n Hemizygote Count Amish Allele Count South Asian \\\n0 0 0 \n1 0 0 \n2 0 1 \n3 0 0 \n4 0 0 \n... ... ... \n11083 0 4 \n11084 0 0 \n11085 0 0 \n11086 0 5 \n11087 0 1 \n\n Allele Number South Asian Homozygote Count South Asian \\\n0 55362 0 \n1 55362 0 \n2 55360 0 \n3 57520 0 \n4 57524 0 \n... ... ... \n11083 88352 0 \n11084 88316 0 \n11085 87828 0 \n11086 87818 0 \n11087 87636 0 \n\n Hemizygote Count South Asian Allele Count Remaining \\\n0 0 0 \n1 0 0 \n2 0 0 \n3 0 1 \n4 0 0 \n... ... ... \n11083 0 8 \n11084 0 0 \n11085 0 0 \n11086 0 0 \n11087 0 0 \n\n Allele Number Remaining Homozygote Count Remaining \\\n0 44082 0 \n1 44082 0 \n2 44162 0 \n3 47700 0 \n4 47678 0 \n... ... ... \n11083 60164 0 \n11084 60142 0 \n11085 59586 0 \n11086 59748 0 \n11087 59608 0 \n\n Hemizygote Count Remaining \n0 0 \n1 0 \n2 0 \n3 0 \n4 0 \n... ... \n11083 0 \n11084 0 \n11085 0 \n11086 0 \n11087 0 \n\n[11088 rows x 72 columns]", - "text/html": "
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gnomAD IDChromosomePositionrsIDsReferenceAlternateSourceFilters - exomesFilters - genomesTranscript...Homozygote Count AmishHemizygote Count AmishAllele Count South AsianAllele Number South AsianHomozygote Count South AsianHemizygote Count South AsianAllele Count RemainingAllele Number RemainingHomozygote Count RemainingHemizygote Count Remaining
06-63720525-A-G663720525rs1768331164AGgnomAD Exomes,gnomAD GenomesPASSPASSENST00000503581.6...000553620004408200
16-63720525-A-T663720525rs1768331164ATgnomAD Genomes<NA>PASSENST00000503581.6...000553620004408200
26-63720526-T-A663720526<NA>TAgnomAD ExomesPASS<NA>ENST00000503581.6...001553600004416200
36-63720531-C-CAA663720531<NA>CCAAgnomAD ExomesPASS<NA>ENST00000503581.6...000575200014770000
46-63720531-C-G663720531rs927390284CGgnomAD Exomes,gnomAD GenomesPASSPASSENST00000503581.6...000575240004767800
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110836-65495478-G-A665495478rs530118054GAgnomAD Exomes,gnomAD GenomesPASSPASSENST00000503581.6...004883520086016400
110846-65495479-G-A665495479rs1766225632GAgnomAD ExomesPASS<NA>ENST00000503581.6...000883160006014200
110856-65495482-A-G665495482rs1766225707AGgnomAD Exomes,gnomAD GenomesPASSPASSENST00000503581.6...000878280005958600
110866-65495484-T-G665495484rs1766225807TGgnomAD ExomesPASS<NA>ENST00000503581.6...005878180005974800
110876-65495485-T-C665495485<NA>TCgnomAD ExomesPASS<NA>ENST00000503581.6...001876360005960800
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11088 rows × 72 columns

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" - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "from api.data.refactoring import parse_gnomad, set_gnomad_dtypes\n", - "from api import (store_database_for_eys_gene,GNOMAD_PATH)\n", - "\n", - "store_database_for_eys_gene('gnomad', False)\n", - "\n", - "gnomad_data = parse_gnomad(GNOMAD_PATH+'/gnomad_data.csv')\n", - "\n", - "set_gnomad_dtypes(gnomad_data)\n", - "\n", - "gnomad_data" - ], "metadata": { - "collapsed": false, "ExecuteTime": { - "end_time": "2024-08-20T18:43:31.996838Z", - "start_time": "2024-08-20T18:43:30.905943Z" + "end_time": "2024-09-10T13:54:32.598753Z", + "start_time": "2024-09-10T13:54:22.948649Z" } }, - "id": "4ba7fd02a60f5693", - "execution_count": 1 - }, - { "cell_type": "code", "source": [ "from api.data.refactoring import merge_gnomad_lovd, parse_gnomad, set_gnomad_dtypes\n", @@ -4015,14 +280,7 @@ "final_data = merge_gnomad_lovd(lovd_data, gnomad_data)\n", "final_data" ], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-09-03T14:19:14.730427Z", - "start_time": "2024-09-03T14:19:05.969159Z" - } - }, - "id": "dd9b17623f26a07c", + "id": "895c77782fbf2e21", "outputs": [ { "name": "stdout", @@ -4474,14 +732,12 @@ "execution_count": 1 }, { + "metadata": {}, "cell_type": "code", "outputs": [], - "source": [], - "metadata": { - "collapsed": false - }, - "id": "50b0e50e88fa0914", - "execution_count": null + "execution_count": null, + "source": "", + "id": "a84eee9bd9b294c9" } ], "metadata": {