From d79310e41fdaed58c9590eb3bb964698af98103a Mon Sep 17 00:00:00 2001 From: Dainius Kirsnauskas Date: Mon, 13 May 2024 19:00:37 +0300 Subject: [PATCH] vcf --- data_collection/refactoring.py | 30 + tests/pipeline.ipynb | 3775 +++++++++++++++++++++++++++++++- 2 files changed, 3790 insertions(+), 15 deletions(-) diff --git a/data_collection/refactoring.py b/data_collection/refactoring.py index fb647fd..28678e9 100644 --- a/data_collection/refactoring.py +++ b/data_collection/refactoring.py @@ -125,3 +125,33 @@ def from_clinvar_name_to_cdna_position(name): break return name[start:end] + + +def save_lovd_as_vcf(df, save_to): + """ + Gets hg38 variants from LOVD and saves as VCF file. + :param DataFrame df: LOVD DataFrame with data + :param str save_to: path where to save VCF file. + """ + + if "VariantOnGenome/DNA/hg38" not in df.columns: + raise ValueError("VariantOnGenome/DNA/hg38 is not in the LOVD DataFrame.") + + save_to_dir = os.path.dirname(save_to) + if not os.path.exists(save_to_dir): + os.makedirs(save_to_dir) + + with open(save_to, "w", encoding="UTF-8") as f: + header = ("##fileformat=VCFv4.2\n" + "##contig=\n" + "#CHROM POS ID REF ALT QUAL FILTER INFO\n") + f.write(header) + for variant in df.loc[:, "VariantOnGenome/DNA/hg38"]: + if len(variant) != 13 or variant[-2] != '>': + logging.warning("Skipping variant %s", variant) + continue + record = ["6", variant[2:-3], ".", variant[-3], variant[-1], ".", ".", "."] + + f.write("\t".join(record)) + f.write("\n") + diff --git a/tests/pipeline.ipynb b/tests/pipeline.ipynb index d2a2fcc..4575606 100644 --- a/tests/pipeline.ipynb +++ b/tests/pipeline.ipynb @@ -2,49 +2,2467 @@ "cells": [ { "cell_type": "code", - "execution_count": null, "id": "initial_id", "metadata": { - "collapsed": true + "collapsed": true, + "ExecuteTime": { + "end_time": "2024-05-13T15:38:18.029744Z", + "start_time": "2024-05-13T15:38:17.807980Z" + } }, - "outputs": [], "source": [ + "import pandas as pd\n", + "\n", "from data_collection import (store_database_for_eys_gene,\n", " parse_lovd,\n", " LOVD_PATH,\n", - " set_lovd_dtypes)" - ] + " set_lovd_dtypes)\n", + "from data_collection.refactoring import save_lovd_as_vcf\n", + "pd.options.display.max_columns = 0" + ], + "outputs": [], + "execution_count": 1 }, { "cell_type": "code", - "outputs": [], "source": [ "store_database_for_eys_gene(\"lovd\", override=False)" ], "metadata": { - "collapsed": false + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-05-13T15:08:35.710520Z", + "start_time": "2024-05-13T15:08:35.708264Z" + } }, "id": "f49f7691a27aa7b4", - "execution_count": null + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "The file at ../data/lovd/lovd_data.txt already exists.\n" + ] + } + ], + "execution_count": 2 }, { "cell_type": "code", + "source": "data = parse_lovd(LOVD_PATH + \"/lovd_data.txt\")", + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-05-13T15:38:24.591752Z", + "start_time": "2024-05-13T15:38:19.498594Z" + } + }, + "id": "cf5c45c0f7b9de0f", "outputs": [], + "execution_count": 2 + }, + { + "metadata": { + "ExecuteTime": { + "end_time": "2024-05-13T15:12:07.510712Z", + "start_time": "2024-05-13T15:12:07.366319Z" + } + }, + "cell_type": "code", "source": [ - "data = parse_lovd(LOVD_PATH + \"/lovd_data.txt\")\n", "for i in data:\n", " print(i)\n", " display(data[i])" ], - "metadata": { - "collapsed": false - }, - "id": "cf5c45c0f7b9de0f", - "execution_count": null + "id": "8a089e29bfc8c119", + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Genes\n" + ] + }, + { + "data": { + "text/plain": [ + " id name ... updated_by updated_date\n", + "0 EYS eyes shut homolog (Drosophila) ... 0 2024-04-19 20:27:30\n", + "\n", + "[1 rows x 34 columns]" + ], + "text/html": [ + "
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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
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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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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
.......................................
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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....................................
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" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "execution_count": 8 }, { "cell_type": "code", - "outputs": [], "source": [ "set_lovd_dtypes(data)\n", "for i in data:\n", @@ -55,7 +2473,1334 @@ "collapsed": false }, "id": "ef07740b2fa63e42", + "outputs": [], "execution_count": null + }, + { + "metadata": { + "ExecuteTime": { + "end_time": "2024-05-13T15:38:25.149624Z", + "start_time": "2024-05-13T15:38:24.807199Z" + } + }, + "cell_type": "code", + "source": "save_lovd_as_vcf(data[\"Variants_On_Genome\"], \"./lovd.vcf\")", + "id": "c968af1617be40db", + "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", + "WARNING:root:Skipping variant g.64902422_64902438del\n", + "WARNING:root:Skipping variant g.64902422_64902438del\n", + "WARNING:root:Skipping variant g.64840707_64997105del\n", + "WARNING:root:Skipping variant g.64840707_64997105del\n", + "WARNING:root:Skipping variant g.64840707_64997105del\n", + "WARNING:root:Skipping variant g.65295915del\n", + "WARNING:root:Skipping variant g.65295915del\n", + "WARNING:root:Skipping variant g.65295915del\n", + "WARNING:root:Skipping variant g.65057728_65320715del\n", + "WARNING:root:Skipping variant g.65057728_65320715del\n", + "WARNING:root:Skipping variant g.65057728_65320715del\n", + "WARNING:root:Skipping variant g.64066349del\n", + "WARNING:root:Skipping variant g.65384425del\n", + "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 g.64439165del\n", + "WARNING:root:Skipping variant g.64439165del\n", + "WARNING:root:Skipping variant g.64626122del\n", + "WARNING:root:Skipping variant g.65494867del\n", + "WARNING:root:Skipping variant \n", + "WARNING:root:Skipping variant g.65494867del\n", + "WARNING:root:Skipping variant \n", + "WARNING:root:Skipping variant g.65494988_65495003del\n", + "WARNING:root:Skipping variant g.63720919_63720920del\n", + "WARNING:root:Skipping variant g.63720668dup\n", + "WARNING:root:Skipping variant g.63720919_63720920del\n", + "WARNING:root:Skipping variant g.63720668dup\n", + "WARNING:root:Skipping variant g.63999116del\n", + "WARNING:root:Skipping variant g.64591039_64591042del\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.64822643dup\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.65495005_65495008delinsAAG\n", + "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", 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{ + "end_time": "2024-05-13T15:58:47.868055Z", + "start_time": "2024-05-13T15:58:41.380466Z" + } + }, + "cell_type": "code", + "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": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "2024-05-13 18:58:41.794056: I tensorflow/core/util/port.cc:113] oneDNN custom operations are on. 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" + } + ], + "execution_count": 4 + }, + { + "metadata": {}, + "cell_type": "code", + "outputs": [], + "execution_count": null, + "source": "", + "id": "6a424607361ab528" } ], "metadata": {