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fix: issue warnings instead of errors when trying to check the header of hap files and issue error when output of transform is not provided to simphenotype #254

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merged 3 commits into from
Aug 7, 2024
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fix: issue warnings instead of errors when trying to check the header of hap files and issue error when output of transform is not provided to simphenotype #254

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317c9b4
treat soft errors as warnings instead
aryarm Jun 28, 2024
2dd6685
fix gt warning in simphenotype and convert to error
aryarm Aug 2, 2024
bc1f7ae
refmt for black
aryarm Aug 2, 2024
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11 changes: 8 additions & 3 deletions haptools/data/haplotypes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -861,7 +861,7 @@ def check_header(
Whether to also check the version of the file
softly: bool, optional
If True, then this function will not raise any ValueErrors. Instead, it
will only issue errors via the logging module, which may be ignored.
will only issue warnings via the logging module, which may be ignored.

Raises
------
Expand All @@ -881,7 +881,7 @@ def check_header(
if softly:

def err_msgr(msg):
self.log.error(msg)
self.log.warning(msg)

else:

Expand Down Expand Up @@ -932,7 +932,12 @@ def err_msgr(msg):
)
# if there are any fields left...
if any(exp_extras.values()):
names = [n for name in exp_extras.values() for n in name]
names = tuple(
f"#{t} {tval}"
for t in exp_extras
for tval in exp_extras[t]
if exp_extras[t]
)
err_msgr(
"Expected the input .hap file to have these extra fields, but they "
f"don't seem to be declared in the header: {*names,}"
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4 changes: 2 additions & 2 deletions haptools/sim_phenotype.py
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Original file line number Diff line number Diff line change
Expand Up @@ -444,10 +444,10 @@ def simulate_pt(
gt = Genotypes.merge_variants((gt, tr_gt), fname=None)

# check that all of the genotypes were loaded successfully and warn otherwise
if len(haplotype_ids) < len(gt.variants):
if len(haplotype_ids) > len(gt.variants):
diff = list(haplotype_ids.difference(gt.variants["id"]))
first_few = 5 if len(diff) > 5 else len(diff)
log.warning(
log.error(
f"{len(diff)} effects could not be found in the genotypes file. Check "
"that the IDs in your .snplist or .hap file correspond with those in the "
"genotypes file. Here are the first few missing variants: "
Expand Down
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