diff options
Diffstat (limited to 'wqflask/base/data_set.py')
| -rwxr-xr-x | wqflask/base/data_set.py | 50 |
1 files changed, 44 insertions, 6 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 30221503..cf219fda 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -16,8 +16,6 @@ # Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) # at rwilliams@uthsc.edu and xzhou15@uthsc.edu # -#we -# # This module is used by GeneNetwork project (www.genenetwork.org) from __future__ import absolute_import, print_function, division @@ -27,6 +25,7 @@ import string import collections import json +import gzip import cPickle as pickle import itertools @@ -52,8 +51,6 @@ from pprint import pformat as pf DS_NAME_MAP = {} def create_dataset(dataset_name, dataset_type = None): - - print("dataset_type:", dataset_type) if not dataset_type: dataset_type = Dataset_Getter(dataset_name) #dataset_type = get_dataset_type_from_json(dataset_name) @@ -129,7 +126,7 @@ def create_datasets_list(): for result in g.db.execute(query).fetchall(): #The query at the beginning of this function isn't necessary here, but still would #rather just reuse it - print("type: {}\tname: {}".format(dataset_type, result.Name)) + #print("type: {}\tname: {}".format(dataset_type, result.Name)) dataset = create_dataset(result.Name, dataset_type) datasets.append(dataset) @@ -261,6 +258,36 @@ class DatasetGroup(object): if maternal and paternal: self.parlist = [maternal, paternal] + def get_sample_list(self): + genofilename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno')) + genofile = open(genofilename, "r") + for line in genofile: + line = line.strip() + if line.startswith(("#", "@")): + continue + headline = line + break + headers = headline.split("\t") + if headers[3] == "Mb": + self.samplelist = headers[4:] + else: + self.samplelist = headers[3:] + + #if genotype_1.type == "group" and self.parlist: + # genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1) + #else: + # genotype_2 = genotype_1 + + #determine default genotype object + #if self.incparentsf1 and genotype_1.type != "intercross": + # genotype = genotype_2 + #else: + # self.incparentsf1 = 0 + # genotype = genotype_1 + + #self.samplelist = list(genotype.prgy) + + def read_genotype_file(self): '''Read genotype from .geno file instead of database''' #if self.group == 'BXD300': @@ -275,7 +302,18 @@ class DatasetGroup(object): # reaper barfs on unicode filenames, so here we ensure it's a string full_filename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno')) - genotype_1.read(full_filename) + if os.path.isfile(full_filename): + print("Reading file: ", full_filename) + genotype_1.read(full_filename) + print("File read") + else: + try: + full_filename = str(os.path.join(webqtlConfig.TMPDIR, self.name + '.geno')) + #print("Reading file") + genotype_1.read(full_filename) + #print("File read") + except IOError: + print("File doesn't exist!") if genotype_1.type == "group" and self.parlist: genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1) |