diff options
Diffstat (limited to 'wqflask/base/data_set.py')
| -rwxr-xr-x | wqflask/base/data_set.py | 80 |
1 files changed, 60 insertions, 20 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 17881e53..ab8554a0 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -35,6 +35,7 @@ from base import webqtlConfig from base import species from dbFunction import webqtlDatabaseFunction from utility import webqtlUtil +from utility.benchmark import Bench from MySQLdb import escape_string as escape from pprint import pformat as pf @@ -73,14 +74,60 @@ class Markers(object): self.markers = json.load(json_data_fh) 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): marker['p_value'] = 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): + + def __init__(self, name): + marker_data_fh = open(os.path.join(webqtlConfig.PYLMM_PATH + name + '.bim')) + self.markers = [] + for line in marker_data_fh: + splat = line.strip().split() + 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)) + def add_pvalues(self, p_values): + #for marker, p_value in itertools.izip(self.markers, p_values): + # if marker['Mb'] <= 0 and marker['chr'] == 0: + # continue + # marker['p_value'] = 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 + + 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 + + + class DatasetGroup(object): """ Each group has multiple datasets; each species has multiple groups. @@ -104,21 +151,17 @@ class DatasetGroup(object): self.incparentsf1 = False self.allsamples = None - self.markers = Markers(self.name) - - - #def read_genotype(self): - # self.read_genotype_file() - # - # if not self.genotype: # Didn'd succeed, so we try method 2 - # self.read_genotype_data() + + + def get_markers(self): + print("self.species is:", self.species) + if self.species == "human": + marker_class = HumanMarkers + else: + marker_class = Markers - #def read_genotype_json(self): - # '''Read genotype from json file''' - # - # json_data = open(os.path.join(webqtlConfig.NEWGENODIR + self.name + '.json')) - # markers = json.load(json_data) - # + self.markers = marker_class(self.name) + def get_f1_parent_strains(self): try: @@ -321,12 +364,9 @@ class PhenotypeDataSet(DataSet): continue # for now if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users): description = this_trait.pre_publication_description - this_trait.description_display = description - - try: - this_trait.description_display.decode('ascii') - except Exception: - this_trait.description_display = this_trait.description_display.decode('utf-8') + this_trait.description_display = description.decode('utf-8') + + if not this_trait.year.isdigit(): this_trait.pubmed_text = "N/A" |