diff options
Diffstat (limited to 'wqflask/base/data_set.py')
| -rwxr-xr-x | wqflask/base/data_set.py | 85 |
1 files changed, 59 insertions, 26 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index f4ca3ae0..a2b13748 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -167,28 +167,56 @@ class Markers(object): marker['Mb'] = float(marker['Mb']) self.markers = markers - print("self.markers:", self.markers) + #print("self.markers:", self.markers) def add_pvalues(self, p_values): print("length of self.markers:", len(self.markers)) print("length of p_values:", len(p_values)) - # THIS IS only needed for the case when we are limiting the number of p-values calculated - if len(self.markers) < len(p_values): - self.markers = self.markers[:len(p_values)] - - for marker, p_value in itertools.izip(self.markers, p_values): - if not p_value: - continue - marker['p_value'] = float(p_value) - if math.isnan(marker['p_value']) or 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 type(p_values) is list: + # THIS IS only needed for the case when we are limiting the number of p-values calculated + #if len(self.markers) > len(p_values): + # self.markers = self.markers[:len(p_values)] + + for marker, p_value in itertools.izip(self.markers, p_values): + if not p_value: + continue + marker['p_value'] = float(p_value) + if math.isnan(marker['p_value']) or 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 + elif type(p_values) is dict: + filtered_markers = [] + for marker in self.markers: + #print("marker[name]", marker['name']) + #print("p_values:", p_values) + if marker['name'] in p_values: + #print("marker {} IS in p_values".format(i)) + marker['p_value'] = p_values[marker['name']] + if math.isnan(marker['p_value']) or (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 + filtered_markers.append(marker) + #else: + #print("marker {} NOT in p_values".format(i)) + #self.markers.remove(marker) + #del self.markers[i] + self.markers = filtered_markers + + #for i, marker in enumerate(self.markers): + # if not 'p_value' in marker: + # #print("self.markers[i]", self.markers[i]) + # del self.markers[i] + # #self.markers.remove(self.markers[i]) class HumanMarkers(Markers): @@ -226,15 +254,15 @@ class HumanMarkers(Markers): # #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 - print("p_values2:", p_values) + #print("p_values2:", pf(p_values)) super(HumanMarkers, self).add_pvalues(p_values) - with Bench("deleting markers"): - markers = [] - for marker in self.markers: - if not marker['Mb'] <= 0 and not marker['chr'] == 0: - markers.append(marker) - self.markers = markers + #with Bench("deleting markers"): + # markers = [] + # for marker in self.markers: + # if not marker['Mb'] <= 0 and not marker['chr'] == 0: + # markers.append(marker) + # self.markers = markers @@ -254,7 +282,7 @@ class DatasetGroup(object): self.name = "BXD" self.f1list = None - self.parlist = None + self.parlist = None self.get_f1_parent_strains() #print("parents/f1s: {}:{}".format(self.parlist, self.f1list)) @@ -476,8 +504,9 @@ class DataSet(object): else: self.samplelist = self.group.samplelist - if (self.group.parlist + self.group.f1list) in self.samplelist: - self.samplelist += self.group.parlist + self.group.f1list + if self.group.parlist != None and self.group.f1list != None: + 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 @@ -547,7 +576,11 @@ class DataSet(object): order by {}.Id """.format(*mescape(self.type, self.type, self.type, self.type, self.name, dataset_type, self.type, self.type, dataset_type)) + + #print("trait data query: ", query) + results = g.db.execute(query).fetchall() + #print("query results:", results) trait_sample_data.append(results) trait_count = len(trait_sample_data[0]) |