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author | Frederick Muriuki Muriithi | 2024-02-05 15:18:44 +0300 |
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committer | Frederick Muriuki Muriithi | 2024-02-05 15:43:25 +0300 |
commit | 3f879d120f7628646f383a457206b15037cc57dc (patch) | |
tree | eaecac8299eeabef511f0297ac439ae0cf590a4e /r_qtl/r_qtl2.py | |
parent | 3245182e967f5ac8a296cf47ce3e622c3cb754ed (diff) | |
download | gn-uploader-3f879d120f7628646f383a457206b15037cc57dc.tar.gz |
Check that data in geno file is valid
Add a function to ensure the values in the geno files are all listed
in the control data under the "genotypes" key.
Diffstat (limited to 'r_qtl/r_qtl2.py')
-rw-r--r-- | r_qtl/r_qtl2.py | 4 |
1 files changed, 2 insertions, 2 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py index f8c08d9..e74312f 100644 --- a/r_qtl/r_qtl2.py +++ b/r_qtl/r_qtl2.py @@ -10,7 +10,7 @@ import yaml from functional_tools import take, chain -from r_qtl.errors import InvalidFormat +from r_qtl.errors import InvalidFormat, MissingFileError __FILE_TYPES__ = ( "geno", "founder_geno", "pheno", "covar", "phenocovar", "gmap", "pmap", @@ -250,7 +250,7 @@ def file_data(zfile: ZipFile, zfile, member_key, cdata, process_transposed_value): yield row except KeyError as exc: - raise InvalidFormat(*exc.args) from exc + raise MissingFileError(*exc.args) from exc def cross_information(zfile: ZipFile, cdata: dict) -> Iterator[dict]: """Load cross information where present.""" |