diff options
Diffstat (limited to 'wqflask/base/data_set.py')
| -rwxr-xr-x | wqflask/base/data_set.py | 46 |
1 files changed, 35 insertions, 11 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 3deaa655..f4ca3ae0 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -23,6 +23,7 @@ import os import math import string import collections +import codecs import json import gzip @@ -156,18 +157,30 @@ class Markers(object): """Todo: Build in cacheing so it saves us reading the same file more than once""" def __init__(self, name): json_data_fh = open(os.path.join(webqtlConfig.NEWGENODIR + name + '.json')) - self.markers = json.load(json_data_fh) + markers = json.load(json_data_fh) + + for marker in markers: + if (marker['chr'] != "X") and (marker['chr'] != "Y"): + marker['chr'] = int(marker['chr']) + else: + marker['chr'] = 19 + marker['Mb'] = float(marker['Mb']) + + self.markers = 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)) + 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): - marker['p_value'] = p_value + 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 @@ -179,16 +192,25 @@ class Markers(object): class HumanMarkers(Markers): - def __init__(self, name): + def __init__(self, name, specified_markers = []): marker_data_fh = open(os.path.join(webqtlConfig.PYLMM_PATH + name + '.bim')) self.markers = [] for line in marker_data_fh: splat = line.strip().split() #print("splat:", splat) - marker = {} - marker['chr'] = int(splat[0]) - marker['name'] = splat[1] - marker['Mb'] = float(splat[3]) / 1000000 + if len(specified_markers) > 0: + if splat[1] in specified_markers: + marker = {} + marker['chr'] = int(splat[0]) + marker['name'] = splat[1] + marker['Mb'] = float(splat[3]) / 1000000 + else: + continue + else: + marker = {} + marker['chr'] = int(splat[0]) + marker['name'] = splat[1] + marker['Mb'] = float(splat[3]) / 1000000 self.markers.append(marker) #print("markers is: ", pf(self.markers)) @@ -241,6 +263,8 @@ class DatasetGroup(object): self.incparentsf1 = False self.allsamples = None + def get_specified_markers(self, markers = []): + self.markers = HumanMarkers(self.name, markers) def get_markers(self): #print("self.species is:", self.species) @@ -954,8 +978,8 @@ class MrnaAssayDataSet(DataSet): #XZ, 12/08/2008: description #XZ, 06/05/2009: Rob asked to add probe target description - description_string = str(this_trait.description).strip() - target_string = str(this_trait.probe_target_description).strip() + description_string = unicode(str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8') + target_string = unicode(str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') if len(description_string) > 1 and description_string != 'None': description_display = description_string |