From bdde44925e4403c26d061ca85fea5b320ed22a59 Mon Sep 17 00:00:00 2001 From: Arya Massarat <23412689+aryarm@users.noreply.github.com> Date: Mon, 4 Nov 2024 19:59:22 +0000 Subject: [PATCH 1/2] start on mergestr recursion test. TODO: create test files --- trtools/mergeSTR/tests/test_mergeSTR.py | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/trtools/mergeSTR/tests/test_mergeSTR.py b/trtools/mergeSTR/tests/test_mergeSTR.py index 1e8e1406..97e347b2 100644 --- a/trtools/mergeSTR/tests/test_mergeSTR.py +++ b/trtools/mergeSTR/tests/test_mergeSTR.py @@ -272,6 +272,31 @@ def test_GetInfoItem(capsys): retval = GetInfoItem(dummy_records, [True, True, False, False], 'END') assert retval == "END=120" +def test_mergeSTR_recursion(args, vcfdir, mrgvcfdir, tmpdir): + # Test that mergeSTR will accept its own output as input + # Create a merged VCF and then merge it again with a different file + fname1 = os.path.join(mrgvcfdir, "CEU_test_subset1.vcf.gz") + fname2 = os.path.join(mrgvcfdir, "CEU_test_subset2.vcf.gz") + args.vcftype = "hipstr" + + # create a single merged file + merged = str(tmpdir / "test-CEU-subset1") + args.out = merged + args.vcfs = fname1 + "," + fname2 + args.vcfs_list = None + assert main(args)==0 + + fname1 = merged + fname2 = os.path.join(mrgvcfdir, "CEU_test_subset3.vcf.gz") + args.vcftype = "hipstr" + + # create a single merged file + merged = str(tmpdir / "test-CEU-subset2") + args.out = merged + args.vcfs = fname1 + "," + fname2 + args.vcfs_list = None + assert_same_vcf(args.out + '.vcf', vcfdir + "/CEU_test.vcf.gz") + # TODO write WriteSampleData tests """ From dc3c57c8ef11d9e223d69828cb48afef8286f5b8 Mon Sep 17 00:00:00 2001 From: Arya Massarat <23412689+aryarm@users.noreply.github.com> Date: Mon, 4 Nov 2024 23:35:51 +0000 Subject: [PATCH 2/2] try to create initial version of test headers are not identical still --- trtools/mergeSTR/tests/test_mergeSTR.py | 64 +- .../sample_vcfs/mergeSTR_vcfs/CEU_test.vcf | 3420 +++++++++++++++++ .../mergeSTR_vcfs/CEU_test_subset10.vcf.gz | Bin 0 -> 40111 bytes .../CEU_test_subset10.vcf.gz.tbi | Bin 0 -> 135 bytes .../mergeSTR_vcfs/CEU_test_subset150.vcf.gz | Bin 0 -> 45398 bytes .../CEU_test_subset150.vcf.gz.tbi | Bin 0 -> 135 bytes .../mergeSTR_vcfs/CEU_test_subset19.vcf.gz | Bin 0 -> 40505 bytes .../CEU_test_subset19.vcf.gz.tbi | Bin 0 -> 135 bytes 8 files changed, 3457 insertions(+), 27 deletions(-) create mode 100644 trtools/testsupport/sample_vcfs/mergeSTR_vcfs/CEU_test.vcf create mode 100644 trtools/testsupport/sample_vcfs/mergeSTR_vcfs/CEU_test_subset10.vcf.gz create mode 100644 trtools/testsupport/sample_vcfs/mergeSTR_vcfs/CEU_test_subset10.vcf.gz.tbi create mode 100644 trtools/testsupport/sample_vcfs/mergeSTR_vcfs/CEU_test_subset150.vcf.gz create mode 100644 trtools/testsupport/sample_vcfs/mergeSTR_vcfs/CEU_test_subset150.vcf.gz.tbi create mode 100644 trtools/testsupport/sample_vcfs/mergeSTR_vcfs/CEU_test_subset19.vcf.gz create mode 100644 trtools/testsupport/sample_vcfs/mergeSTR_vcfs/CEU_test_subset19.vcf.gz.tbi diff --git a/trtools/mergeSTR/tests/test_mergeSTR.py b/trtools/mergeSTR/tests/test_mergeSTR.py index 97e347b2..9dff3940 100644 --- a/trtools/mergeSTR/tests/test_mergeSTR.py +++ b/trtools/mergeSTR/tests/test_mergeSTR.py @@ -1,9 +1,11 @@ -import argparse import os +import shutil +import argparse +import subprocess import cyvcf2 -import numpy as np import pytest +import numpy as np from ..mergeSTR import * from trtools.testsupport.utils import assert_same_vcf @@ -272,31 +274,6 @@ def test_GetInfoItem(capsys): retval = GetInfoItem(dummy_records, [True, True, False, False], 'END') assert retval == "END=120" -def test_mergeSTR_recursion(args, vcfdir, mrgvcfdir, tmpdir): - # Test that mergeSTR will accept its own output as input - # Create a merged VCF and then merge it again with a different file - fname1 = os.path.join(mrgvcfdir, "CEU_test_subset1.vcf.gz") - fname2 = os.path.join(mrgvcfdir, "CEU_test_subset2.vcf.gz") - args.vcftype = "hipstr" - - # create a single merged file - merged = str(tmpdir / "test-CEU-subset1") - args.out = merged - args.vcfs = fname1 + "," + fname2 - args.vcfs_list = None - assert main(args)==0 - - fname1 = merged - fname2 = os.path.join(mrgvcfdir, "CEU_test_subset3.vcf.gz") - args.vcftype = "hipstr" - - # create a single merged file - merged = str(tmpdir / "test-CEU-subset2") - args.out = merged - args.vcfs = fname1 + "," + fname2 - args.vcfs_list = None - assert_same_vcf(args.out + '.vcf', vcfdir + "/CEU_test.vcf.gz") - # TODO write WriteSampleData tests """ @@ -397,6 +374,39 @@ def test_popstr_output(args, mrgvcfdir): assert main(args) == 0 assert_same_vcf(args.out + '.vcf', mrgvcfdir + "/popstr_merged.vcf") +def test_mergeSTR_recursion(args, mrgvcfdir, tmpdir): + # Test that mergeSTR will accept its own output as input + # Create a merged VCF and then merge it again with a different file + + if shutil.which("bgzip") is not None and shutil.which("tabix") is not None: + # First, merge two files of 10 and 19 samples, respectively + fname1 = os.path.join(mrgvcfdir, "CEU_test_subset10.vcf.gz") + fname2 = os.path.join(mrgvcfdir, "CEU_test_subset19.vcf.gz") + args.vcftype = "hipstr" + merged = str(tmpdir / "test-CEU-subset1") + args.out = merged + args.vcfs = fname1 + "," + fname2 + args.vcfs_list = None + assert main(args)==0 + subprocess.run(["bgzip", merged + ".vcf"]) + subprocess.run(["tabix", "-p", "vcf", merged + ".vcf.gz"]) + else: + merged = str(mrgvcfdir / "test-CEU-subset1") + + # Now, merge the output of mergeSTR with another file of 150 samples + fname1 = merged + ".vcf.gz" + fname2 = os.path.join(mrgvcfdir, "CEU_test_subset150.vcf.gz") + args.vcftype = "hipstr" + merged = str(tmpdir / "test-CEU-subset2") + args.out = merged + args.vcfs = fname1 + "," + fname2 + args.vcfs_list = None + assert main(args)==0 + + # The subsetted files were created by subsetting CEU_test.vcf.gz, so they should end up the same + # { zcat CEU_test.vcf.gz | head -n-3 && zcat CEU_test.vcf.gz | cut -f -9,10-19; } | bgzip > CEU_test_subset10.vcf.gz + assert_same_vcf(args.out + '.vcf', mrgvcfdir + "/CEU_test.vcf") + # TODO questions and issues to confirm, test or address: # confirm conflicting samples cause this to fail unless --update-sample-from-file is given diff --git a/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/CEU_test.vcf b/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/CEU_test.vcf new file mode 100644 index 00000000..cf1c8b35 --- /dev/null +++ b/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/CEU_test.vcf @@ -0,0 +1,3420 @@ +##fileformat=VCFv4.1 +##FILTER= +##command=HipSTR-v0.6.2 --bams 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.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL 2|7:3|5:0.99:0.49:31:0:1:3:15.52|15.48:0|0:2.05:-0:17:0:-11|1;-5|2;0|1;3|9;5|6:3|8;5|7:PASS 2|7:3|5:1:0.5:24:0:0:3:13.40|10.60:0|0:10.55:-0.22:15:0:-15|2;-5|1;0|3;3|5;5|6:3|7;5|5:PASS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL 2|14:3|5:1:0.5:24:0:5:2:11.21|12.79:0|0:2.48:0:19:0:-15|1;-5|3;3|7;5|11:3|7;5|10:PASS 5|7:4|5:1:0.5:35:0:2:5:18.12|16.88:0|0:3.41:-0.17:23:-0.47:-16|2;-5|1;-4|1;0|1;3|1;4|10;5|12;7|1:-1|1;4|11;5|9;7|1:PASS 7|12:5|5:1:0.5:25:0:0:3:16.43|8.57:0|0:3.58:-0.94:20:-0.94:-4|1;0|2;5|13;6|1;37|1:5|13:PASS 5|7:4|5:1:0.5:30:0:0:2:16.08|13.92:0|0:6.97:-0.09:18:-0.2:-15|1;-5|1;-4|1;0|4;4|7;5|6:4|9;5|6:PASS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL 7|4:5|3:0.98:0.49:21:0:8:2:15.58|5.42:0|0:2.06:-1.51:18:-0:0|1;2|1;3|7;5|6:2|1;3|7;5|5;9|1:PASS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL 7|12:5|5:0.95:0.48:29:0:5:4:20.94|8.06:0|0:1.29:-1.97:23:-0.26:-17|1;-4|1;0|2;3|4;5|10:3|2;4|1;5|8:PASS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL 2|2:3|3:1:1:33:0:2:0:16.50|16.50:0|0:2.85:0:.:0:-21|2;0|1;3|18:3|17:PASS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL 7|11:5|5:1:0.5:29:0:0:3:20.04|8.96:0|0:2.89:-1.72:19:-0.28:-15|2;-13|1;-6|1;0|1;5|14;6|1:5|14:PASS 7|13:5|5:1:0.5:39:0:1:3:26.65|12.35:0|0:5.08:-1.9:28:-0.85:-15|1;-4|1;-3|1;0|2;5|22;6|2;7|1:5|24;6|1:PASS 7|12:5|5:1:0.5:39:0:0:2:26.32|12.68:0|0:3.48:-1.9:28:-0.54:-13|1;-4|1;0|1;5|23:5|20:PASS 2|10:3|5:0.76:0.38:29:0:1:4:17.13|11.87:0|0:0.51:-0.37:25:-0.2:-5|1;-4|1;0|1;3|11;5|9;7|1:3|11;5|8:PASS 7|11:5|5:1:0.5:30:0:1:4:20.10|9.90:0|0:8.15:-1.36:25:-0.86:-15|1;-13|1;-11|1;-5|2;-3|1;5|16;7|1:5|17:PASS 7|11:5|5:0.61:0.3:34:0:7:4:25.92|8.08:0|0:0.19:-2.82:27:-0.91:-15|3;0|1;3|9;5|9;11|1:3|7;5|10:PASS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL 7|11:5|5:1:0.5:32:0:1:2:22.56|9.44:0|0:3.95:-1.97:23:-0.91:-5|2;0|3;5|14:5|16;6|1:PASS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL 2|7:3|5:1:0.5:38:0:1:4:16.84|21.16:0|0:8.46:-0.15:27:-0.39:0|3;3|13;4|1;5|13:3|12;4|1;5|13:PASS 2|3:3|3:1:0.5:28:0:1:2:20.33|7.67:0|0:7.4:-1.83:25:-0.56:-5|2;3|18;4|1:3|16;4|1:PASS 7|13:5|5:1:0.5:23:0:0:1:17.50|5.50:0|0:2.83:-1.93:20:0:-15|2;-5|2;5|13:5|13:PASS 2|3:3|3:0.86:0.43:28:0:0:2:21.95|6.05:0|0:0.81:-2.6:26:-0.26:-5|3;-3|1;3|19:3|19:PASS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL 2|7:3|5:1:0.5:35:0:1:3:19.66|15.34:0|0:13.2:-0.24:28:-0.99:-15|1;-5|2;0|1;3|15;5|10;14|1:3|15;5|11:PASS 2|7:3|5:1:0.5:21:0:1:3:8.42|12.58:0|0:4.93:-0.37:14:0:-15|1;-5|1;0|1;3|6;5|8:3|6;5|7:PASS 7|12:5|5:1:0.5:26:0:2:3:15.25|10.75:0|0:3.7:-0.39:23:-0.6:-15|3;-5|1;0|4;3|1;4|1;5|14;14|1:3|1;4|1;5|16:PASS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL 2|7:3|5:1:0.5:33:0:3:4:14.71|18.29:0|0:8.7:-0.3:20:0:-3|1;0|1;3|9;4|1;5|10;7|1:3|9;4|2;5|9:PASS 7|12:5|5:1:0.5:36:0:1:2:23.09|12.91:0|0:4.31:-1.01:30:-2.8:-15|1;-13|1;-5|3;0|2;5|22;6|1:5|23;6|1:PASS 3|5:3|4:0.99:0.5:24:0:3:1:8.60|15.40:0|0:2.29:-0.78:19:-0.29:-16|1;0|1;3|9;4|5:3|9;4|4:PASS 7|7:5|5:0.34:0.34:31:0:0:4:15.50|15.50:0|0:-0.28:0:.:0:-15|3;-5|1;-4|1;5|18:5|17:PASS 2|7:3|5:0.99:0.5:24:0:0:2:13.38|10.62:0|0:2.23:-0.34:16:-1.45:-15|1;-4|1;0|1;3|10;5|5;14|1:3|10;5|4:PASS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL 7|12:5|5:0.72:0.36:33:0:1:2:22.24|10.76:0|0:0.42:-1.21:29:-1.57:-15|1;-5|2;-2|1;0|1;4|1;5|21:4|1;5|20:PASS 5|7:4|5:1:0.5:20:0:1:1:11.13|8.87:0|0:9.28:-0:15:0:-16|1;-15|2;-11|1;0|2;4|5;5|4:4|6;5|4:PASS 7|10:5|5:0.86:0.43:27:0:0:1:20.37|6.63:0|0:1.02:-2.18:24:-0.88:-15|1;-5|1;0|2;5|18:5|19:PASS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL 7|12:5|5:1:0.5:45:0:3:3:29.41|15.59:0|0:5.09:-1.39:35:-1.43:-15|3;-13|1;-5|2;-1|1;0|1;4|1;5|22;13|1;14|1:1|1;4|1;5|25;6|1:PASS 7|13:5|5:1:0.5:35:0:1:3:25.42|9.58:0|0:4.9:-2.43:28:-0.85:-5|1;0|3;5|22;13|1:5|22;6|1:PASS 7|10:5|5:0.95:0.47:30:0:1:3:21.59|8.41:0|0:1.28:-1.9:28:-0.54:-17|1;0|1;5|20;6|1:5|18:PASS 0|7:0|5:1:0.5:29:0:1:2:14.18|14.82:0|0:9.89:0:24:-0.23:0|13;5|10:-1|1;0|9;5|11:PASS 7|12:5|5:1:0.5:32:0:0:3:21.95|10.05:0|0:4.36:-1.72:27:-0.55:-15|1;-5|1;0|1;5|22;6|1:5|22:PASS 0|7:0|5:0.93:0.47:40:0:2:4:21.11|18.89:0|0:1.14:-0.07:28:-0.22:0|16;5|12;6|1:-5|1;0|13;5|10;6|1:PASS 5|7:4|5:1:0.5:33:0:1:1:15.84|17.16:0|0:2.52:0:21:-0.51:4|10;5|10;7|1:4|10;5|9;7|1:PASS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL 0|7:0|5:1:0.5:35:0:0:5:15.57|19.43:0|0:7.46:-0.42:21:-0.49:-18|1;-13|1;0|11;5|10;6|1:0|8;5|10:PASS 7|13:5|5:0.52:0.26:22:0:0:1:16.97|5.03:0|0:0.04:-2.12:18:-0.61:-15|3;-3|1;0|3;5|8:5|11:PASS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL 2|11:3|5:0.65:0.32:20:0:3:3:12.27|7.73:0|0:0.27:-0.57:13:-0.64:-11|1;-5|1;0|2;2|1;3|3;4|1;5|5:2|1;3|4;5|4:PASS 7|14:5|5:0.9:0.45:33:0:0:3:23.35|9.65:0|0:0.97:-1.83:25:-0.86:-18|1;-15|1;-10|1;-5|1;5|22;14|1:5|21:PASS 2|7:3|5:1:0.5:28:0:0:3:16.21|11.79:0|0:4.09:-0.62:18:-0.28:3|12;4|1;5|8:3|12;5|6:PASS 7|14:5|5:1:0.5:28:0:7:4:20.30|7.70:0|0:6.44:-1.64:24:-1.62:-17|1;-15|2;-11|1;-5|2;0|4;4|7;5|5;13|1:4|6;5|8:PASS 2|2:3|3:0.65:0.65:37:0:2:5:18.50|18.50:0|0:0.42:0:.:0:-17|1;-15|1;-5|1;-4|1;0|1;2|1;3|19;4|1;12|1:3|18;4|1:PASS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL 2|7:3|5:1:0.5:27:0:0:2:14.56|12.44:0|0:5.48:-0.19:19:-0.18:0|2;3|11;5|6;6|1:3|10;5|8:PASS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL 2|7:3|5:0.97:0.49:24:0:2:1:8.85|15.15:0|0:1.6:-0.84:17:0:-15|1;0|5;3|3;4|1;5|7;6|1:3|4;4|1;5|9;6|1:PASS 7|12:5|5:1:0.5:37:0:1:2:27.66|9.34:0|0:2.77:-2.84:30:-0.85:-11|1;-5|1;0|1;5|24;6|1;7|1:5|25:PASS 2|3:3|3:1:0.5:23:0:0:3:14.46|8.54:0|0:9.83:-0.58:20:-0.28:-15|1;-5|2;3|15:3|12:PASS 2|14:3|5:0.79:0.39:29:0:5:4:16.48|12.52:0|0:0.58:-0.28:22:-1.34:-15|1;0|4;3|7;5|8;7|1;12|1:3|9;5|8:PASS 5|7:4|5:1:0.5:39:0:0:4:22.25|16.75:0|0:5.49:-0.77:26:-0.58:-15|1;-5|1;0|2;4|17;5|9:4|16;5|8:PASS 7|11:5|5:1:0.5:34:0:9:3:21.64|12.36:0|0:8.63:-1.06:28:-2.55:-19|1;-16|1;-15|2;-5|2;-3|1;0|1;4|6;5|13;7|2:4|6;5|15;9|1:PASS 2|7:3|5:0.91:0.45:23:0:0:2:8.44|14.56:0|0:1:-0.62:18:0:3|7;5|13:3|6;5|12:PASS 7|12:5|5:0.96:0.48:24:0:0:2:17.90|6.10:0|0:1.38:-1.77:22:-0.27:-15|1;-5|1;0|1;5|14;13|1:5|15:PASS 2|5:3|4:0.94:0.47:27:0:2:1:16.51|10.49:0|0:1.22:-0.58:20:0:-5|1;0|2;3|13;4|6:3|13;4|5:PASS 2|2:3|3:1:1:41:0:0:5:20.50|20.50:0|0:3.16:0:.:0:-17|1;-5|2;0|4;3|24;6|1;11|1;14|1:3|22:PASS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL 2|10:3|5:0.98:0.49:38:0:3:4:22.78|15.22:0|0:1.67:-0.79:33:0:-13|1;0|1;3|17;4|2;5|10:3|16;4|2;5|8:PASS 2|7:3|5:1:0.5:31:0:3:1:16.52|14.48:0|0:9.55:-0.09:18:-0.74:-17|1;0|2;3|9;4|3;5|5:3|9;4|3;5|5:PASS 7|12:5|5:0.88:0.44:27:0:0:3:21.57|5.43:0|0:0.95:-3.31:23:-0.28:-15|3;-13|2;-6|1;-4|1;-3|1;0|3;5|14:5|17:PASS 7|12:5|5:1:0.5:29:0:1:3:18.92|10.08:0|0:7.91:-0.91:27:-0.28:-15|2;-3|1;0|1;5|18;6|1:1|1;5|20:PASS .:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL 7|14:5|5:0.97:0.49:35:0:0:1:27.63|7.37:0|0:1.76:-3.49:30:-0.85:-15|2;-5|3;0|2;5|19:5|21:PASS 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