diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 13 |
1 files changed, 7 insertions, 6 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 017c6052..091433a6 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -168,7 +168,8 @@ class Markers(object): for marker, p_value in itertools.izip(self.markers, p_values): marker['p_value'] = p_value - print("p_value is:", marker['p_value']) + 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 @@ -436,7 +437,7 @@ class DataSet(object): except TypeError: print("Dataset {} is not yet available in GeneNetwork.".format(self.name)) pass - + def get_trait_data(self): self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list query = """ @@ -493,12 +494,12 @@ class DataSet(object): if self.type == "Publish": query += """ - WHERE {}XRef.InbredSetId = {}Freeze.InbredSetId + WHERE {}XRef.PublicationId = {}Freeze.Id and {}Freeze.Name = '{}' - and {}.Id = {}XRef.PhenotypeId + and {}.Id = {}XRef.{}Id order by {}.Id - """.format(*mescape(self.type, self.type, self.type, self.name, - dataset_type, self.type, dataset_type )) + """.format(*mescape(self.type, self.type, self.type, self.type, + self.name, dataset_type, self.type, self.type, dataset_type)) else: query += """ WHERE {}XRef.{}FreezeId = {}Freeze.Id |