ensure the current directory is used for all output from make_dosages

gymrek-lab · Oct 31, 2023 · 09289ea · 09289ea
1 parent 1fdf8e5
commit 09289ea
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/trtools/testsupport/sample_vcfs/associaTR/make_dosages.py b/trtools/testsupport/sample_vcfs/associaTR/make_dosages.py
@@ -17,7 +17,7 @@
 vcf = cyvcf2.VCF(str(SCRIPT_DIR / 'many_samples_biallelic.vcf.gz'))
 samples = vcf.samples
 
-with open('gp_dosages.tsv', 'w') as gp_out, open('ap1_dosages.tsv', 'w') as ap1_out, open('ap2_dosages.tsv', 'w') as ap2_out:
+with open(str(SCRIPT_DIR / 'gp_dosages.tsv'), 'w') as gp_out, open(str(SCRIPT_DIR / 'ap1_dosages.tsv'), 'w') as ap1_out, open(str(SCRIPT_DIR / 'ap2_dosages.tsv'), 'w') as ap2_out:
     for var in vcf:
         gp_out.write('{}\t{}\t{}'.format(var.CHROM, var.POS, var.POS))
         ap1_out.write('{}\t{}\t{}'.format(var.CHROM, var.POS, var.POS))
@@ -98,7 +98,7 @@
 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:
+with open(str(SCRIPT_DIR / 'ap1_multi_dosages.tsv'), 'w') as ap1_out, open(str(SCRIPT_DIR / 'ap2_multi_dosages.tsv'), 'w') as ap2_out:
     for var in vcf:
         ap1_out.write('{}\t{}\t{}'.format(var.CHROM, var.POS, var.POS))
         ap2_out.write('{}\t{}\t{}'.format(var.CHROM, var.POS, var.POS))