From 048bbf7e4ee49fece9652dad401f40b6a865e1a9 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 24 Sep 2015 17:13:19 +0000
Subject: Location range feature should work for correlations now, though the
interface appearance needs to be improved
---
wqflask/wqflask/correlation/show_corr_results.py | 39 +++++++++++++++++++---
.../show_trait_calculate_correlations.html | 14 ++++++++
2 files changed, 49 insertions(+), 4 deletions(-)
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 6a120325..63a7a555 100755
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -110,6 +110,17 @@ class CorrelationResults(object):
self.min_expr = float(start_vars['min_expr'])
self.p_range_lower = float(start_vars['p_range_lower'])
self.p_range_upper = float(start_vars['p_range_upper'])
+ self.min_location_chr = start_vars['min_loc_chr']
+ self.max_location_chr = start_vars['max_loc_chr']
+ if start_vars['min_loc_mb'].isdigit():
+ self.min_location_mb = start_vars['min_loc_mb']
+ else:
+ self.min_location_mb = 0
+ if start_vars['max_loc_mb'].isdigit():
+ self.max_location_mb = start_vars['max_loc_mb']
+ else:
+ self.max_location_mb = 1000
+ self.max_location = [start_vars['max_loc_chr'], start_vars['max_loc_mb']]
self.get_formatted_corr_type()
self.return_number = int(start_vars['corr_return_results'])
@@ -167,15 +178,35 @@ class CorrelationResults(object):
key=lambda t: -abs(t[1][0])))
+ #ZS: Convert min/max chromosome to an int for the location range option
+ min_chr_as_int = 1
+ max_chr_as_int = 30 #Just to make sure all are included if user inputs nothing
+ for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems():
+ if chr_info.name == self.min_location_chr:
+ min_chr_as_int = order_id
+ if chr_info.name == self.max_location_chr:
+ max_chr_as_int = order_id
+
for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]):
print("trait name:", trait)
trait_object = GeneralTrait(dataset=self.target_dataset, name=trait, get_qtl_info=True)
- print("trait_object.mean:", trait_object.mean)
- print("self.min_expr:", self.min_expr)
- print("self.p_range_upper:", self.p_range_upper)
+
+ #ZS: Convert trait chromosome to an int for the location range option
+ chr_as_int = 0
+ for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems():
+ if chr_info.name == trait_object.chr:
+ chr_as_int = order_id
+
if (float(trait_object.mean) > self.min_expr and
float(self.correlation_data[trait][0]) > self.p_range_lower and
- float(self.correlation_data[trait][0]) < self.p_range_upper):
+ float(self.correlation_data[trait][0]) < self.p_range_upper and
+ chr_as_int >= min_chr_as_int and
+ chr_as_int <= max_chr_as_int):
+
+ if (chr_as_int == min_chr_as_int and float(trait_object.mb) < float(self.min_location_mb)):
+ continue
+ elif (chr_as_int == max_chr_as_int and float(trait_object.mb) > float(self.max_location_mb)):
+ continue
(trait_object.sample_r,
trait_object.sample_p,
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index cefe9763..65b9d08e 100755
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -79,6 +79,20 @@
+