From 1fdf8e5cb445469e3eab26d5956efe1c8b5d8802 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Tue, 31 Oct 2023 14:40:50 -0700
Subject: [PATCH] try to execute all of make_dosages.py in its dir

---
 trtools/testsupport/sample_vcfs/associaTR/make_dosages.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/trtools/testsupport/sample_vcfs/associaTR/make_dosages.py b/trtools/testsupport/sample_vcfs/associaTR/make_dosages.py
index d9f0c181..a53233f1 100755
--- a/trtools/testsupport/sample_vcfs/associaTR/make_dosages.py
+++ b/trtools/testsupport/sample_vcfs/associaTR/make_dosages.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
-import pathlib
 import random
+import pathlib
 
 import cyvcf2
 import numpy as np
@@ -91,11 +91,11 @@
     'tabix -f many_samples_biallelic_dosages.vcf.gz '
     '"'
 )
-sp.run(cmd, shell = True, check=True)
+sp.run(cmd, shell = True, check=True, cwd=str(SCRIPT_DIR))
 
 # multiallelic
 
-vcf = cyvcf2.VCF('many_samples_multiallelic.vcf.gz')
+vcf = cyvcf2.VCF(str(SCRIPT_DIR / 'many_samples_multiallelic.vcf.gz'))
 samples = vcf.samples
 
 with open('ap1_multi_dosages.tsv', 'w') as ap1_out, open('ap2_multi_dosages.tsv', 'w') as ap2_out:
@@ -142,5 +142,5 @@
     'tabix -f many_samples_multiallelic_dosages.vcf.gz '
     '"'
 )
-sp.run(cmd, shell = True, check=True)
+sp.run(cmd, shell = True, check=True, cwd=str(SCRIPT_DIR))