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| author | Frederick Muriuki Muriithi | 2024-01-10 08:00:25 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-01-10 08:02:52 +0300 |
| commit | a4313e2cc0f8548946186838a4ce67e358e46bbe (patch) | |
| tree | e59e844775ec8992b8bbecb78bc291e8bf25079e | |
| parent | 0d0b284a76bee863b97c46e8275cd62e02552a93 (diff) | |
| download | gn-uploader-a4313e2cc0f8548946186838a4ce67e358e46bbe.tar.gz | |
Provide convenience functions to avoid subtle call errors
| -rw-r--r-- | r_qtl/r_qtl2.py | 5 | ||||
| -rw-r--r-- | scripts/rqtl2/install_genotypes.py | 6 |
2 files changed, 6 insertions, 5 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py index d8231bb..b2a7acf 100644 --- a/r_qtl/r_qtl2.py +++ b/r_qtl/r_qtl2.py @@ -289,3 +289,8 @@ def validate_bundle(zfile: ZipFile): __member_exists_p__(zfile, cdata["cross_info"]["file"]) except KeyError as kerr: raise InvalidFormat(*kerr.args) from kerr + +def genotype_data(zfile: ZipFile): + """Convenience function to genotype data from R/qtl2 bundle.""" + cdata = control_data(zfile) + return file_data(zfile, "geno", cdata, *make_process_data_geno(cdata)) diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py index a555d46..6ae3788 100644 --- a/scripts/rqtl2/install_genotypes.py +++ b/scripts/rqtl2/install_genotypes.py @@ -132,11 +132,7 @@ def install_genotypes(dbconn: mdb.Connection, logger.info(("Loading genotypes. This could take a while. " "Please be patient.")) - cdata = rqtl2.control_data(zfile) - genotypes = rqtl2.file_data(zfile, - "geno", - cdata, - rqtl2.make_process_data_geno(cdata)) + genotypes = rqtl2.genotype_data(zfile) while True: batch = tuple(take(genotypes, 5000)) if len(batch) == 0: |