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Resolves #34 #35

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Merged
ofrei merged 1 commit into from
May 18, 2022
Merged

Resolves #34 #35

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6 changes: 3 additions & 3 deletions gwas/gwas.py
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Original file line number Diff line number Diff line change
Expand Up @@ -390,7 +390,7 @@ def make_regenie_merge_commands(args, logistic):
cmd = ''
for pheno in args.pheno:
cmd += '$PYTHON gwas.py merge-regenie ' + \
pass_arguments_along(args, ['info-file', 'info', 'maf', 'hwe', 'geno']) + \
pass_arguments_along(args, ['info-file', 'info', 'maf', 'hwe', 'geno', 'config']) + \
' --sumstats {out}_chr@_{pheno}.regenie'.format(out=args.out, pheno=pheno) + \
' --basename {out}_chr@'.format(out=args.out) + \
' --out {out}_{pheno} '.format(out=args.out, pheno=pheno) + \
Expand All @@ -403,7 +403,7 @@ def make_saige_merge_commands(args, logistic, array_spec):
use_chunks = (args.chunk_size_bp is not None)
for pheno in args.pheno:
cmd += '$PYTHON gwas.py merge-saige ' + \
pass_arguments_along(args, ['info-file', 'info', 'maf', 'hwe', 'geno']) + \
pass_arguments_along(args, ['info-file', 'info', 'maf', 'hwe', 'geno', 'config']) + \
(' --sumstats {out}_chr@_{pheno}.saige'.format(out=args.out, pheno=pheno) if (not use_chunks) else "") + \
(' --sumstats {out}_chunk@_{pheno}.saige'.format(out=args.out, pheno=pheno) if use_chunks else "") + \
' --basename {out}_chr@'.format(out=args.out) + \
Expand All @@ -417,7 +417,7 @@ def make_plink2_merge_commands(args, logistic):
cmd = ''
for pheno in args.pheno:
cmd += '$PYTHON gwas.py merge-plink2 ' + \
pass_arguments_along(args, ['info-file', 'info', 'maf', 'hwe', 'geno']) + \
pass_arguments_along(args, ['info-file', 'info', 'maf', 'hwe', 'geno', 'config']) + \
' --sumstats {out}_chr@.{pheno}.glm.{what}'.format(out=args.out, pheno=pheno, what=('logistic' if logistic else 'linear')) + \
' --basename {out}_chr@'.format(out=args.out) + \
' --out {out}_{pheno} '.format(out=args.out, pheno=pheno) + \
Expand Down