diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/r_qtl/test_r_qtl2_qc.py | 98 |
1 files changed, 65 insertions, 33 deletions
diff --git a/tests/r_qtl/test_r_qtl2_qc.py b/tests/r_qtl/test_r_qtl2_qc.py index 554cfc4..d12172e 100644 --- a/tests/r_qtl/test_r_qtl2_qc.py +++ b/tests/r_qtl/test_r_qtl2_qc.py @@ -18,27 +18,44 @@ from quality_control.errors import InvalidValue ("tests/r_qtl/test_files/empty_control_file_json.zip", tuple()), ("tests/r_qtl/test_files/allfilesmissing_stringmembers.zip", - ("geno.csv", "fgeno.csv", "pheno.csv", "covar.csv", "phenocovar.csv", - "gmap.csv", "pmap.csv", "phenose.csv", "sex.csv", "crossinfo.csv")), + (("geno", "geno.csv"), ("founder_geno", "fgeno.csv"), + ("pheno", "pheno.csv"), ("covar", "covar.csv"), + ("phenocovar", "phenocovar.csv"), ("gmap", "gmap.csv"), + ("pmap", "pmap.csv"), ("phenose", "phenose.csv"), + ("sex.file", "sex.csv"), ("cross_info.file", "crossinfo.csv"))), ("tests/r_qtl/test_files/allfilesmissing_listmembers.zip", - ("geno01.csv", "geno02.csv", "fgeno01.csv", "fgeno02.csv", "fgeno03.csv", - "pheno01.csv", "pheno02.csv", "covar01.csv", "covar02.csv", - "phenocovar01.csv", "phenocovar02.csv", "phenocovar03.csv", - "phenocovar04.csv", "gmap01.csv", "gmap02.csv", "pmap01.csv", "pmap02.csv", - "phenose01.csv", "phenose02.csv", "sex01.csv", "sex02.csv", "sex03.csv", - "crossinfo01.csv", "crossinfo02.csv")), + (("geno", "geno01.csv"), ("geno", "geno02.csv"), + ("founder_geno", "fgeno01.csv"), ("founder_geno", "fgeno02.csv"), + ("founder_geno", "fgeno03.csv"), ("pheno", "pheno01.csv"), + ("pheno", "pheno02.csv"), ("covar", "covar01.csv"), + ("covar", "covar02.csv"), ("phenocovar", "phenocovar01.csv"), + ("phenocovar", "phenocovar02.csv"), ("phenocovar", "phenocovar03.csv"), + ("phenocovar", "phenocovar04.csv"), ("gmap", "gmap01.csv"), + ("gmap", "gmap02.csv"), ("pmap", "pmap01.csv"), ("pmap", "pmap02.csv"), + ("phenose", "phenose01.csv"), ("phenose", "phenose02.csv"), + ("sex.file", "sex01.csv"), ("sex.file", "sex02.csv"), + ("sex.file", "sex03.csv"), ("cross_info.file", "crossinfo01.csv"), + ("cross_info.file", "crossinfo02.csv"))), ("tests/r_qtl/test_files/allfilesmissing_mixedmembers.zip", - ("geno01.csv", "geno02.csv", "fgeno01.csv", "fgeno02.csv", "fgeno03.csv", - "pheno01.csv", "pheno02.csv", "covar.csv", "phenocovar.csv", - "gmap01.csv", "gmap02.csv", "pmap01.csv", "pmap02.csv", "phenose01.csv", - "phenose02.csv", "sex01.csv", "sex02.csv", "sex03.csv", - "crossinfo.csv")), + (("geno", "geno01.csv"), ("geno", "geno02.csv"), + ("founder_geno", "fgeno01.csv"), ("founder_geno", "fgeno02.csv"), + ("founder_geno", "fgeno03.csv"), ("pheno", "pheno01.csv"), + ("pheno", "pheno02.csv"), ("covar", "covar.csv"), + ("phenocovar", "phenocovar.csv"), ("gmap", "gmap01.csv"), + ("gmap", "gmap02.csv"), ("pmap", "pmap01.csv"), ("pmap", "pmap02.csv"), + ("phenose", "phenose01.csv"), ("phenose", "phenose02.csv"), + ("sex.file", "sex01.csv"), ("sex.file", "sex02.csv"), + ("sex.file", "sex03.csv"), ("cross_info.file", "crossinfo.csv"))), ("tests/r_qtl/test_files/somefilesmissing_mixedmembers.zip", - ("geno01.csv", "geno02.csv", "fgeno01.csv", "fgeno02.csv", "fgeno03.csv", - "pheno01.csv", "pheno02.csv", "covar.csv", "phenocovar.csv", - "gmap01.csv", "gmap02.csv", "pmap01.csv", "pmap02.csv", "phenose01.csv", - "phenose02.csv", "sex01.csv", "sex02.csv", "sex03.csv", - "crossinfo.csv")))) + (("geno", "geno01.csv"), ("geno", "geno02.csv"), + ("founder_geno", "fgeno01.csv"), ("founder_geno", "fgeno02.csv"), + ("founder_geno", "fgeno03.csv"), ("pheno", "pheno01.csv"), + ("pheno", "pheno02.csv"), ("covar", "covar.csv"), + ("phenocovar", "phenocovar.csv"), ("gmap", "gmap01.csv"), + ("gmap", "gmap02.csv"), ("pmap", "pmap01.csv"), ("pmap", "pmap02.csv"), + ("phenose", "phenose01.csv"), ("phenose", "phenose02.csv"), + ("sex.file", "sex01.csv"), ("sex.file", "sex02.csv"), + ("sex.file", "sex03.csv"), ("cross_info.file", "crossinfo.csv"))))) def test_bundle_files_list(filepath, expected): """ GIVEN: R/qtl2 bundle with a control file listing files @@ -56,24 +73,39 @@ def test_bundle_files_list(filepath, expected): ("tests/r_qtl/test_files/empty_control_file_json.zip", tuple()), ("tests/r_qtl/test_files/allfilesmissing_stringmembers.zip", - ("geno.csv", "fgeno.csv", "pheno.csv", "covar.csv", "phenocovar.csv", - "gmap.csv", "pmap.csv", "phenose.csv", "sex.csv", "crossinfo.csv")), + (("geno", "geno.csv"), ("founder_geno", "fgeno.csv"), + ("pheno", "pheno.csv"), ("covar", "covar.csv"), + ("phenocovar", "phenocovar.csv"), ("gmap", "gmap.csv"), + ("pmap", "pmap.csv"), ("phenose", "phenose.csv"), + ("sex.file", "sex.csv"), ("cross_info.file", "crossinfo.csv"))), ("tests/r_qtl/test_files/allfilesmissing_listmembers.zip", - ("geno01.csv", "geno02.csv", "fgeno01.csv", "fgeno02.csv", "fgeno03.csv", - "pheno01.csv", "pheno02.csv", "covar01.csv", "covar02.csv", - "phenocovar01.csv", "phenocovar02.csv", "phenocovar03.csv", - "phenocovar04.csv", "gmap01.csv", "gmap02.csv", "pmap01.csv", "pmap02.csv", - "phenose01.csv", "phenose02.csv", "sex01.csv", "sex02.csv", "sex03.csv", - "crossinfo01.csv", "crossinfo02.csv")), + (("geno", "geno01.csv"), ("geno", "geno02.csv"), + ("founder_geno", "fgeno01.csv"), ("founder_geno", "fgeno02.csv"), + ("founder_geno", "fgeno03.csv"), ("pheno", "pheno01.csv"), + ("pheno", "pheno02.csv"), ("covar", "covar01.csv"), + ("covar", "covar02.csv"), ("phenocovar", "phenocovar01.csv"), + ("phenocovar", "phenocovar02.csv"), ("phenocovar", "phenocovar03.csv"), + ("phenocovar", "phenocovar04.csv"), ("gmap", "gmap01.csv"), + ("gmap", "gmap02.csv"), ("pmap", "pmap01.csv"), ("pmap", "pmap02.csv"), + ("phenose", "phenose01.csv"), ("phenose", "phenose02.csv"), + ("sex.file", "sex01.csv"), ("sex.file", "sex02.csv"), + ("sex.file", "sex03.csv"), ("cross_info.file", "crossinfo01.csv"), + ("cross_info.file", "crossinfo02.csv"))), ("tests/r_qtl/test_files/allfilesmissing_mixedmembers.zip", - ("geno01.csv", "geno02.csv", "fgeno01.csv", "fgeno02.csv", "fgeno03.csv", - "pheno01.csv", "pheno02.csv", "covar.csv", "phenocovar.csv", - "gmap01.csv", "gmap02.csv", "pmap01.csv", "pmap02.csv", "phenose01.csv", - "phenose02.csv", "sex01.csv", "sex02.csv", "sex03.csv", - "crossinfo.csv")), + (("geno", "geno01.csv"), ("geno", "geno02.csv"), + ("founder_geno", "fgeno01.csv"), ("founder_geno", "fgeno02.csv"), + ("founder_geno", "fgeno03.csv"), ("pheno", "pheno01.csv"), + ("pheno", "pheno02.csv"), ("covar", "covar.csv"), + ("phenocovar", "phenocovar.csv"), ("gmap", "gmap01.csv"), + ("gmap", "gmap02.csv"), ("pmap", "pmap01.csv"), ("pmap", "pmap02.csv"), + ("phenose", "phenose01.csv"), ("phenose", "phenose02.csv"), + ("sex.file", "sex01.csv"), ("sex.file", "sex02.csv"), + ("sex.file", "sex03.csv"), ("cross_info.file", "crossinfo.csv"))), ("tests/r_qtl/test_files/somefilesmissing_mixedmembers.zip", - ("fgeno01.csv", "covar.csv", "gmap01.csv", "gmap02.csv", "pmap01.csv", - "pmap02.csv", "phenose02.csv", "sex03.csv", "crossinfo.csv")))) + (("founder_geno", "fgeno01.csv"), ("covar", "covar.csv"), + ("gmap", "gmap01.csv"), ("gmap", "gmap02.csv"), ("pmap", "pmap01.csv"), + ("pmap", "pmap02.csv"), ("phenose", "phenose02.csv"), + ("sex.file", "sex03.csv"), ("cross_info.file", "crossinfo.csv"))))) def test_missing_files(filepath, expected): """ GIVEN: R/qtl2 bundle with a control file listing files |