diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 20 |
1 files changed, 11 insertions, 9 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index beb62bd7..9fa7beb3 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) |