diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/marker_regression/rqtl_mapping.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/run_mapping.py | 10 |
2 files changed, 9 insertions, 6 deletions
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index 09afb8d1..121ce53b 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, model, method, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, cofactors): +def run_rqtl(trait_name, vals, samples, dataset, pair_scan, 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, dataset, cofactors, perm_strata_list) @@ -38,6 +38,9 @@ def run_rqtl(trait_name, vals, samples, dataset, mapping_scale, model, method, n "scale": mapping_scale } + if pair_scan: + post_data["pair_scan"] = True + if do_control == "true" and control_marker: post_data["control_marker"] = control_marker diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 8b9f89d2..6c1c92cb 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -232,19 +232,19 @@ class RunMapping: self.score_type = "LOD" self.control_marker = start_vars['control_marker'] self.do_control = start_vars['do_control'] - if 'mapmethod_rqtl_geno' in start_vars: - self.method = start_vars['mapmethod_rqtl_geno'] + if 'mapmethod_rqtl' in start_vars: + self.method = start_vars['mapmethod_rqtl'] else: self.method = "em" - self.model = start_vars['mapmodel_rqtl_geno'] + self.model = start_vars['mapmodel_rqtl'] self.pair_scan = False if 'pair_scan' in start_vars: 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.model, self.method, self.num_perm, self.perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates) + self.this_trait.name, self.vals, self.samples, self.dataset, self.pair_scan, self.mapping_scale, self.model, self.method, self.num_perm, self.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.model, self.method, + results = rqtl_mapping.run_rqtl(self.this_trait.name, self.vals, self.samples, self.dataset, self.pair_scan, self.mapping_scale, self.model, self.method, self.num_perm, self.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 |