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print failed commands
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@omerwe
omerwe committed Nov 12, 2023
1 parent 5f1460d commit 2770f2c
Showing 1 changed file with 26 additions and 21 deletions.
47 changes: 26 additions & 21 deletions test_polyfun.py
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Original file line number Diff line number Diff line change
Expand Up @@ -98,9 +98,10 @@ def test_munge_sumstats(tmpdir, python3_exe):
output_file = os.path.join(tmpdir, outfile)
gold_file = os.path.join(gold_dir, outfile)

retval = os.system('%s %s --sumstats %s --out %s --n 327209 --min-info 0.6 --min-maf 0.001'%(python3_exe, script_exe, input_file, output_file))
cmd = '%s %s --sumstats %s --out %s --n 327209 --min-info 0.6 --min-maf 0.001'%(python3_exe, script_exe, input_file, output_file)
retval = os.system(cmd)
if retval != 0:
raise ValueError('munge_sumstats command failed')
raise ValueError('munge_sumstats command failed when running the following command:\n%s'%(cmd))

compare_dfs(tmpdir, gold_dir, outfile)

Expand All @@ -123,26 +124,29 @@ def test_polyfun(tmpdir, python3_exe):
plink_prefix = os.path.join(example_dir, 'reference.')

#polyfun stage 2
retval = os.system('%s %s --compute-h2-L2 --output-prefix %s --sumstats %s --ref-ld-chr %s --w-ld-chr %s --nnls-exact'%
(python3_exe, script_exe, output_prefix, sumstats_file, ref_ld_prefix, w_ld_prefix))
cmd = '%s %s --compute-h2-L2 --output-prefix %s --sumstats %s --ref-ld-chr %s --w-ld-chr %s --nnls-exact' % \
(python3_exe, script_exe, output_prefix, sumstats_file, ref_ld_prefix, w_ld_prefix)
retval = os.system(cmd)
if retval != 0:
raise ValueError('PolyFun command failed')
raise ValueError('PolyFun command failed when running the following command:\n%s'%(cmd))
for outfile in ['testrun.22.bins.parquet', 'testrun.22.snpvar_ridge_constrained.gz', 'testrun.22.snpvar_ridge.gz', 'testrun.22.l2.M']:
compare_dfs(tmpdir, gold_dir, outfile)

#polyfun stage 3
retval = os.system('%s %s --compute-ldscores --output-prefix %s --bfile-chr %s --nnls-exact'%
(python3_exe, script_exe, output_prefix, plink_prefix))
cmd = '%s %s --compute-ldscores --output-prefix %s --bfile-chr %s --nnls-exact'% \
(python3_exe, script_exe, output_prefix, plink_prefix)
retval = os.system(cmd)
if retval != 0:
raise ValueError('PolyFun command failed')
raise ValueError('PolyFun command failed when running the following command:\n%s'%(cmd))

compare_dfs(tmpdir, gold_dir, 'testrun.22.l2.ldscore.parquet')

#polyfun stage 4
retval = os.system('%s %s --compute-h2-bins --output-prefix %s --sumstats %s --w-ld-chr %s --nnls-exact'%
(python3_exe, script_exe, output_prefix, sumstats_file, w_ld_prefix))
cmd = '%s %s --compute-h2-bins --output-prefix %s --sumstats %s --w-ld-chr %s --nnls-exact'% \
(python3_exe, script_exe, output_prefix, sumstats_file, w_ld_prefix)
retval = os.system(cmd)
if retval != 0:
raise ValueError('PolyFun command failed')
raise ValueError('PolyFun command failed when running the following command:\n%s'%(cmd))
compare_dfs(tmpdir, gold_dir, 'testrun.22.snpvar_constrained.gz')


Expand All @@ -164,29 +168,29 @@ def test_polyloc(tmpdir, python3_exe):
posterior_file = os.path.join(example_dir, 'posterior_betas.gz')

#polyloc stage 1
polyloc_cmd = ('%s %s --compute-partitions --output-prefix %s --posterior %s --bfile-chr %s --nnls-exact'%
polyloc_cmd = ('%s %s --compute-partitions --output-prefix %s --posterior %s --bfile-chr %s --nnls-exact'% \
(python3_exe, script_exe, output_prefix, posterior_file, plink_prefix))
retval = os.system(polyloc_cmd)
if retval != 0:
raise ValueError('PolyLoc command failed')
raise ValueError('PolyLoc command failed when running the following command:\n%s'%(polyloc_cmd))
for outfile in ['polyloc_test.22.bins.parquet', 'polyloc_test.22.l2.M']:
compare_dfs(tmpdir, gold_dir, outfile)


#polyloc stage 2
polyloc_cmd = ('%s %s --compute-ldscores --output-prefix %s --bfile-chr %s --nnls-exact'%
polyloc_cmd = ('%s %s --compute-ldscores --output-prefix %s --bfile-chr %s --nnls-exact'% \
(python3_exe, script_exe, output_prefix, plink_prefix))
retval = os.system(polyloc_cmd)
if retval != 0:
raise ValueError('PolyLoc command failed')
raise ValueError('PolyLoc command failed when running the following command:\n%s'%(polyloc_cmd))
compare_dfs(tmpdir, gold_dir, 'polyloc_test.22.l2.ldscore.parquet')

#polyloc stage 3
polyloc_cmd = ('%s %s --compute-polyloc --output-prefix %s --w-ld-chr %s --sumstats %s --nnls-exact'%
polyloc_cmd = ('%s %s --compute-polyloc --output-prefix %s --w-ld-chr %s --sumstats %s --nnls-exact'% \
(python3_exe, script_exe, output_prefix, w_ld_prefix, sumstats_file))
retval = os.system(polyloc_cmd)
if retval != 0:
raise ValueError('PolyLoc command failed')
raise ValueError('PolyLoc command failed when running the following command:\n%s'%(polyloc_cmd))
for outfile in ['polyloc_test.bin_h2', 'polyloc_test.Mp']:
compare_dfs(tmpdir, gold_dir, outfile)

Expand All @@ -205,9 +209,10 @@ def test_extract_snpvar(tmpdir, python3_exe):
output_file = os.path.join(tmpdir, outfile)
gold_file = os.path.join(gold_dir, outfile)

retval = os.system('%s %s --sumstats %s --out %s'%(python3_exe, script_exe, input_file, output_file))
cmd = '%s %s --sumstats %s --out %s'%(python3_exe, script_exe, input_file, output_file)
retval = os.system(cmd)
if retval != 0:
raise ValueError('extract_snpvar command failed')
raise ValueError('extract_snpvar command failed when running the following command:\n%s'%(cmd))
compare_dfs(tmpdir, gold_dir, outfile)


Expand Down Expand Up @@ -244,7 +249,7 @@ def test_finemapper_susie(tmpdir, python3_exe):
#print(finemapper_cmd)
retval = os.system(finemapper_cmd)
if retval != 0:
raise ValueError('finemapper command failed')
raise ValueError('finemapper command failed when running the following command:\n%s'%(cmd))
compare_dfs(tmpdir, gold_dir, outfile, sort_column='SNP')


Expand Down Expand Up @@ -282,7 +287,7 @@ def test_finemapper_finemap(tmpdir, python3_exe, finemap_exe):
#print(finemapper_cmd)
retval = os.system(finemapper_cmd)
if retval != 0:
raise ValueError('finemapper command failed')
raise ValueError('finemapper command failed when running the following command:\n%s'%(cmd))
compare_dfs(tmpdir, gold_dir, outfile, sort_column='SNP')


Expand Down

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