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 %}
<td align="right">{{ '%0.2f' | format(marker.lod_score|float) }}</td>
{% else %}
- <td align="right">{{ '%0.2f' | format(marker.lrs_value|float / 4.16) }}</td>
+ <td align="right">{{ '%0.2f' | format(marker.lrs_value|float / 4.61) }}</td>
{% endif %}
{% else %}
{% if 'lod_score' in marker %}
- <td align="right">{{ '%0.2f' | format(marker.lod_score|float * 4.16) }}</td>
+ <td align="right">{{ '%0.2f' | format(marker.lod_score|float * 4.61) }}</td>
{% else %}
<td align="right">{{ '%0.2f' | format(marker.lrs_value|float) }}</td>
{% endif %}
--
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