From 3325184b1dd310619626dd31852ab84cae6dc7fc Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Tue, 8 Oct 2013 12:13:56 -0500 Subject: Did some work with interval mapping page; will use qtl reaper to do the mapping, since it is reliable/fast and avoids us having to rewrite from scratch using something like r/qtl --- wqflask/base/data_set.py | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) (limited to 'wqflask/base/data_set.py') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 96e04df0..befbd518 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -168,13 +168,13 @@ class Markers(object): for marker, p_value in itertools.izip(self.markers, p_values): marker['p_value'] = p_value - if marker['p_value'] == 0: - marker['lod_score'] = 0 - marker['lrs_value'] = 0 - else: - marker['lod_score'] = -math.log10(marker['p_value']) - #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values - marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 + if math.isnan(marker['p_value']): + print("p_value is:", marker['p_value']) + marker['lod_score'] = -math.log10(marker['p_value']) + #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values + marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 + + class HumanMarkers(Markers): @@ -189,6 +189,8 @@ class HumanMarkers(Markers): marker['name'] = splat[1] marker['Mb'] = float(splat[3]) / 1000000 self.markers.append(marker) + + #print("markers is: ", pf(self.markers)) def add_pvalues(self, p_values): @@ -315,10 +317,10 @@ class DatasetGroup(object): #determine default genotype object if self.incparentsf1 and genotype_1.type != "intercross": - genotype = genotype_2 + self.genotype = genotype_2 else: self.incparentsf1 = 0 - genotype = genotype_1 + self.genotype = genotype_1 self.samplelist = list(genotype.prgy) -- cgit v1.2.3 From a823e66f8dc742e1608b3e0db6d521d5f63b641a Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Tue, 15 Oct 2013 15:06:36 -0500 Subject: Changed templates to call the header macro Correlation page now works with Non-BXD (or whatever group) or All Samples options --- wqflask/base/data_set.py | 14 ++++++++------ wqflask/wqflask/correlation/show_corr_results.py | 4 ++-- wqflask/wqflask/templates/base.html | 4 ++-- wqflask/wqflask/templates/correlation_page.html | 8 ++------ wqflask/wqflask/templates/index_page.html | 2 -- wqflask/wqflask/templates/marker_regression.html | 10 ++-------- wqflask/wqflask/templates/quick_search.html | 11 +++-------- wqflask/wqflask/templates/search_result_page.html | 10 ++-------- wqflask/wqflask/templates/show_trait.html | 11 +++-------- 9 files changed, 24 insertions(+), 50 deletions(-) (limited to 'wqflask/base/data_set.py') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 9fa7beb3..f25e7974 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -322,7 +322,7 @@ class DatasetGroup(object): self.incparentsf1 = 0 self.genotype = genotype_1 - self.samplelist = list(genotype.prgy) + self.samplelist = list(self.genotype.prgy) #class DataSets(object): @@ -440,10 +440,12 @@ class DataSet(object): def get_trait_data(self, sample_list=None): if sample_list: - self.samplelist = sample_list + self.group.parlist + self.group.f1list + self.samplelist = sample_list else: - self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list - + self.samplelist = self.group.samplelist + + if (self.group.parlist + self.group.f1list) in self.samplelist: + self.samplelist += self.group.parlist + self.group.f1list query = """ SELECT Strain.Name, Strain.Id FROM Strain, Species @@ -503,8 +505,8 @@ class DataSet(object): and {}Freeze.Name = '{}' and {}.Id = {}XRef.{}Id order by {}.Id - """.format(*mescape(self.type, self.type, self.type, self.type, - self.name, dataset_type, self.type, self.type, dataset_type)) + """.format(*mescape(self.type, self.type, self.type, self.name, + dataset_type, self.type, dataset_type, dataset_type)) else: query += """ WHERE {}XRef.{}FreezeId = {}Freeze.Id diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index a5c80674..8f23165c 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -178,10 +178,10 @@ class CorrelationResults(object): trait_object.lit_corr = lit_corr_data[trait][1] self.correlation_results.append(trait_object) - if self.corr_type != "lit": + if self.corr_type != "lit" and self.dataset.type == "ProbeSet": self.do_lit_correlation_for_trait_list() - if self.corr_type != "tissue": + if self.corr_type != "tissue" and self.dataset.type == "ProbeSet": self.do_tissue_correlation_for_trait_list() #print("self.correlation_results: ", pf(self.correlation_results)) diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 8efba6a7..a14eeb44 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -29,9 +29,9 @@ {% macro header(main, second) %}
-

Login

+

{{ main }}

- Gain access to GeneNetwork. + {{ second }}

diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index 4d09cf20..7e149506 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -6,12 +6,8 @@ {% endblock %} {% block content %} - -
-
-

Correlation

-
-
+ + {{ header("Correlation", 'Trait: {} Dataset: {}'.format(this_trait.name, dataset.name)) }} diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html index 98682e57..d177a7bd 100644 --- a/wqflask/wqflask/templates/index_page.html +++ b/wqflask/wqflask/templates/index_page.html @@ -3,8 +3,6 @@ {% block content %} - -

GeneNetwork

diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html index 9260acab..64d2e9b7 100644 --- a/wqflask/wqflask/templates/marker_regression.html +++ b/wqflask/wqflask/templates/marker_regression.html @@ -9,14 +9,8 @@ {% endblock %} {% block content %} -
-
-

Marker Regression

-

- {{ this_trait.name }}: {{ this_trait.description_fmt }} -

-
-
+ {{ header("Marker Regression", + '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
diff --git a/wqflask/wqflask/templates/quick_search.html b/wqflask/wqflask/templates/quick_search.html index b0e38708..2f268c5a 100644 --- a/wqflask/wqflask/templates/quick_search.html +++ b/wqflask/wqflask/templates/quick_search.html @@ -2,14 +2,9 @@ {% block title %}QuickSearch Results{% endblock %} {% block content %} -
-
-

QuickSearch Results

-

- GeneNetwork found {{ numify(results|count, "record", "records") }}. -

-
-
+ + {{ header("QuickSearch Results", + 'GeneNetwork found {}.'.format(numify(results|count, "record", "records"))) }}
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 11f68bba..1fe7cce9 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -2,14 +2,8 @@ {% block title %}Search Results{% endblock %} {% block content %} -
-
-

Search Results

-

- GeneNetwork found {{ numify(results|count, "record", "records") }}. -

-
-
+ {{ header("Search Results", + 'GeneNetwork found {}.'.format(numify(results|count, "record", "records"))) }}
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 799245c3..e3c84de7 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -7,14 +7,9 @@ {% endblock %} {% block content %} -
-
-

{{ this_trait.symbol}}

-

- {{ this_trait.name }}: {{ this_trait.description_fmt }} -

-
-
+ {{ header("{}".format(this_trait.symbol), + '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }} +
-- cgit v1.2.3