From c540d661c9603f33b46edf2f6c8fd6b95bab8b38 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 29 Aug 2019 17:09:46 -0500 Subject: Fixed issue where LOD to LRS conversions weren't showing up correctly in the table Fixed issue where non-LOCO GEMMA wasn't working correctly --- .../wqflask/marker_regression/display_mapping_results.py | 10 +++++----- wqflask/wqflask/marker_regression/gemma_mapping.py | 2 +- wqflask/wqflask/marker_regression/run_mapping.py | 16 ++++++++-------- wqflask/wqflask/templates/mapping_results.html | 4 ++-- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 1d5843d4..911219f4 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -229,10 +229,10 @@ class DisplayMappingResults(object): self.covariates = start_vars['covariates'] if 'maf' in start_vars.keys(): self.maf = start_vars['maf'] + if 'output_files' in start_vars.keys(): + self.output_files = start_vars['output_files'] if 'use_loco' in start_vars.keys() and self.mapping_method == "gemma": self.use_loco = start_vars['use_loco'] - if self.use_loco == "True": - self.output_files = start_vars['output_files'] if 'reaper_version' in start_vars.keys() and self.mapping_method == "reaper": self.reaper_version = start_vars['reaper_version'] @@ -1702,7 +1702,7 @@ class DisplayMappingResults(object): #ZS: Needed to pass to genome browser js_data = json.loads(self.js_data) if self.LRS_LOD == "LRS": - js_data['max_score'] = LRS_LOD_Max/4.16 + js_data['max_score'] = LRS_LOD_Max/4.61 else: js_data['max_score'] = LRS_LOD_Max self.js_data = json.dumps(js_data) @@ -2068,9 +2068,9 @@ class DisplayMappingResults(object): ######################################### myCanvas = pid.PILCanvas(size=(400,300)) if 'lod_score' in self.qtlresults[0] and self.LRS_LOD == "LRS": - perm_output = [value*4.16 for value in self.perm_output] + perm_output = [value*4.61 for value in self.perm_output] elif 'lod_score' not in self.qtlresults[0] and self.LRS_LOD == "LOD": - perm_output = [value/4.16 for value in self.perm_output] + perm_output = [value/4.61 for value in self.perm_output] else: perm_output = self.perm_output diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 8d59a392..5b34e837 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -109,7 +109,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf return marker_obs, gwa_output_filename else: marker_obs = parse_loco_output(this_dataset, gwa_output_filename) - return marker_obs + return marker_obs, gwa_output_filename def gen_pheno_txt_file(this_dataset, genofile_name, vals, trait_filename): """Generates phenotype file for GEMMA""" diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index af5d0206..56d901fc 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -181,18 +181,18 @@ class RunMapping(object): self.dataset.group.get_markers() if self.mapping_method == "gemma": self.first_run = True - self.output_files= None + self.output_files = None + if 'output_files' in start_vars: + self.output_files = start_vars['output_files'] if 'first_run' in start_vars: #ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) self.first_run = False - if 'output_files' in start_vars: - self.output_files = start_vars['output_files'] self.score_type = "-log(p)" self.manhattan_plot = True with Bench("Running GEMMA"): if self.use_loco == "True": marker_obs, self.output_files = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files) else: - marker_obs = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run) + marker_obs, self.output_files = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files) results = marker_obs elif self.mapping_method == "rqtl_plink": results = self.run_rqtl_plink() @@ -397,7 +397,7 @@ class RunMapping(object): if self.mapping_method != "gemma": if self.score_type == "LRS": - significant_for_browser = self.significant / 4.16 + significant_for_browser = self.significant / 4.61 else: significant_for_browser = self.significant @@ -521,15 +521,15 @@ def trim_markers_for_figure(markers): else: filtered_markers.append(marker) else: - if marker[score_type] < 4.16: + if marker[score_type] < 4.61: if low_counter % 20 == 0: filtered_markers.append(marker) low_counter += 1 - elif 4.16 <= marker[score_type] < (2*4.16): + elif 4.61 <= marker[score_type] < (2*4.61): if med_counter % 10 == 0: filtered_markers.append(marker) med_counter += 1 - elif (2*4.16) <= marker[score_type] <= (3*4.16): + elif (2*4.61) <= marker[score_type] <= (3*4.61): if high_counter % 2 == 0: filtered_markers.append(marker) high_counter += 1 diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 189f8abc..373bae1e 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -250,11 +250,11 @@ {% if 'lod_score' in marker %} {{ '%0.2f' | format(marker.lod_score|float) }} {% else %} - {{ '%0.2f' | format(marker.lrs_value|float / 4.16) }} + {{ '%0.2f' | format(marker.lrs_value|float / 4.61) }} {% endif %} {% else %} {% if 'lod_score' in marker %} - {{ '%0.2f' | format(marker.lod_score|float * 4.16) }} + {{ '%0.2f' | format(marker.lod_score|float * 4.61) }} {% else %} {{ '%0.2f' | format(marker.lrs_value|float) }} {% endif %} -- cgit v1.2.3