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| author | zsloan | 2021-05-21 20:32:15 +0000 |
|---|---|---|
| committer | zsloan | 2021-05-21 20:32:15 +0000 |
| commit | d2edff1a05a81cd2ca703de940ea2bec5bd1dd10 (patch) | |
| tree | 60d876097ebab9dc0f7f6d3480a029fd826c9252 /wqflask | |
| parent | efbe47b58f6e0b9a4b509a28ec8788a1c6dae343 (diff) | |
| download | genenetwork2-d2edff1a05a81cd2ca703de940ea2bec5bd1dd10.tar.gz | |
Removed a couple unused parameters for run_rqtl
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/marker_regression/rqtl_mapping.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/run_mapping.py | 6 |
2 files changed, 4 insertions, 4 deletions
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index c3f047fc..d18f6a7b 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -20,7 +20,7 @@ logger = utility.logger.getLogger(__name__) GN3_RQTL_URL = "http://localhost:8086/api/rqtl/compute" GN3_TMP_PATH = "/export/local/home/zas1024/genenetwork3/tmp" -def run_rqtl(trait_name, vals, samples, dataset, mapping_scale, method, model, permCheck, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, pair_scan, cofactors): +def run_rqtl(trait_name, vals, samples, dataset, mapping_scale, model, method, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, cofactors): """Run R/qtl by making a request to the GN3 endpoint and reading in the output file(s)""" pheno_file = write_phenotype_file(trait_name, samples, vals, cofactors) diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index be1186c0..d727e3ff 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -243,10 +243,10 @@ class RunMapping: # self.pair_scan = True if self.permCheck and self.num_perm > 0: self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl( - self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates) + self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates) else: - results = rqtl_mapping.run_rqtl(self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, - self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates) + results = rqtl_mapping.run_rqtl(self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, + self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates) elif self.mapping_method == "reaper": if "startMb" in start_vars: # ZS: Check if first time page loaded, so it can default to ON if "additiveCheck" in start_vars: |