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Fix intersection filters (default: no filtering) #33

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merged 5 commits into from
Jul 29, 2024
Merged

Fix intersection filters (default: no filtering) #33

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3423fb8
Bump version
smlmbrt Jul 29, 2024
ff70266
Allow 0 MAF, set default to no filtering.
smlmbrt Jul 29, 2024
39bdee0
Allow complete genotype missingness, set default to no filtering.
smlmbrt Jul 29, 2024
8654999
Typo fix
smlmbrt Jul 29, 2024
dbaed0a
Update docstring
smlmbrt Jul 29, 2024
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2 changes: 1 addition & 1 deletion pgscatalog.match/pyproject.toml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[tool.poetry]
name = "pgscatalog.match"
version = "0.2.2"
version = "0.2.3"
description = "Tools for matching variants in PGS scoring files and target variant information files"
authors = ["Benjamin Wingfield <bwingfield@ebi.ac.uk>", "Samuel Lambert <sl925@medschl.cam.ac.uk>", "Laurent Gil <lg10@sanger.ac.uk>"]
readme = "README.md"
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13 changes: 7 additions & 6 deletions pgscatalog.match/src/pgscatalog/match/cli/intersect_cli.py
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Expand Up @@ -197,8 +197,8 @@ def run_intersect():

PCA_ELIGIBLE = (
PCA_ELIGIBLE
and (aaf2maf(float(vmatch["AAF"])) > args.maf_filter)
and (float(vmatch["F_MISS_DOSAGE"]) < args.vmiss_filter)
and (aaf2maf(float(vmatch["AAF"])) >= args.maf_filter)
and (float(vmatch["F_MISS_DOSAGE"]) <= args.vmiss_filter)
)
vmatch["PCA_ELIGIBLE"] = PCA_ELIGIBLE
if PCA_ELIGIBLE is True:
Expand Down Expand Up @@ -374,15 +374,15 @@ def parse_args(args=None):
parser.add_argument(
"--maf_target",
dest="maf_filter",
default=0.05,
default=0,
type=float,
required=False,
help="Filter: Minimum minor Allele Frequency for PCA eligibility",
)
parser.add_argument(
"--geno_miss",
dest="vmiss_filter",
default=0.1,
default=1,
type=float,
required=False,
help="Filter: Maximum Genotype missingness for PCA eligibility",
Expand All @@ -404,8 +404,9 @@ def _description_text() -> str:
return textwrap.dedent(
"""\
Program to find matched variants (same strand) between a set of reference and target data .pvar/bim files. This
also uses the .afreq and .vmiss files to evaluate whether the variants in the TARGET are suitable for inclusion in
a PCA analysis, while also filtering on strand ambiguity and multi-allelic/INDEL status.
also evaluate whether the variants in the TARGET are suitable for inclusion in a PCA analysis (excludes strand
ambiguous and multi-allelic/INDEL variants), and can also uses the .afreq and .vmiss files exclude variants with
missingness and MAF filters.
"""
)

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