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# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
# as published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU Affero General Public License for more details.
#
# This program is available from Source Forge: at GeneNetwork Project
# (sourceforge.net/projects/genenetwork/).
#
# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
#
#
#
# This module is used by GeneNetwork project (www.genenetwork.org)
#
# Created by GeneNetwork Core Team 2010/08/10
#
# Last updated by GeneNetwork Core Team 2010/10/20
from __future__ import print_function
from pprint import pformat as pf
import string
import os
import reaper
import webqtlConfig
from webqtlCaseData import webqtlCaseData
from utility import webqtlUtil
class webqtlFormData(object):
'Represents data from a WebQTL form page, needed to generate the next page'
attrs = ('formID','group','genotype','samplelist','allsamplelist', 'display_variance'
'suggestive','significance','submitID','identification', 'enablevariance',
'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo')
#XZ: Attention! All attribute values must be picklable!
def __init__(self,
start_vars = None,
req = None):
# Todo: rework this whole thing
for item in webqtlFormData.attrs:
self.__dict__[item] = None
for item in start_vars:
self.__dict__[item] = start_vars[item]
#Todo: This can't be good below...rework
try:
self.remote_ip = req.connection.remote_ip
except:
self.remote_ip = '1.2.3.4'
self.ppolar = None
self.mpolar = None
if self.group:
_f1, _f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.group]
def set_number(stringy):
return int(stringy) if stringy else 2000 # Rob asked to change the default value to 2000
self.nperm = set_number(self.nperm)
self.nboot = set_number(self.nboot)
if self.allsamplelist:
self.allsamplelist = self.allsamplelist.split()
if self.group == 'BXD300':
self.group = 'BXD'
def __getitem__(self, key):
return self.__dict__[key]
def get(self, key, default=None):
if key in self.__dict__:
return self.__dict__[key]
else:
return default
def __str__(self):
rstr = ''
for item in self.attrs:
if item != 'genotype':
rstr += '%s:%s\n' % (item,str(getattr(self,item)))
return rstr
def readGenotype(self):
'''read genotype from .geno file'''
if self.group == 'BXD300':
self.group = 'BXD'
assert self.group, "self.group needs to be set"
#genotype_1 is Dataset Object without parents and f1
#genotype_2 is Dataset Object with parents and f1 (not for intercross)
self.genotype_1 = reaper.Dataset()
full_filename = locate(self.group + '.geno','genotype')
# reaper barfs on unicode filenames, so here we ensure it's a string
full_filename = str(full_filename)
self.genotype_1.read(full_filename)
print("Got to after read")
try:
# NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
_f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.group]
except KeyError:
_f1 = _f12 = _mat = _pat = None
self.genotype_2 = self.genotype_1
if self.genotype_1.type == "group" and _mat and _pat:
self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat) #, F1=_f1)
#determine default genotype object
if self.incparentsf1 and self.genotype_1.type != "intercross":
self.genotype = self.genotype_2
else:
self.incparentsf1 = 0
self.genotype = self.genotype_1
self.samplelist = list(self.genotype.prgy)
self.f1list = []
self.parlist = []
if _f1 and _f12:
self.f1list = [_f1, _f12]
if _mat and _pat:
self.parlist = [_mat, _pat]
def readData(self, samplelist, incf1=None):
'''read user input data or from trait data and analysis form'''
if incf1 == None:
incf1 = []
if not self.genotype:
self.readGenotype()
if not samplelist:
if incf1:
samplelist = self.f1list + self.samplelist
else:
samplelist = self.samplelist
traitfiledata = getattr(self, "traitfile", None)
traitpastedata = getattr(self, "traitpaste", None)
variancefiledata = getattr(self, "variancefile", None)
variancepastedata = getattr(self, "variancepaste", None)
Nfiledata = getattr(self, "Nfile", None)
#### Todo: Rewrite below when we get to someone submitting their own trait #####
def to_float(item):
try:
return float(item)
except ValueError:
return None
print("bottle samplelist is:", samplelist)
if traitfiledata:
tt = traitfiledata.split()
values = map(webqtlUtil.StringAsFloat, tt)
elif traitpastedata:
tt = traitpastedata.split()
values = map(webqtlUtil.StringAsFloat, tt)
else:
print("mapping formdataasfloat")
#values = map(self.FormDataAsFloat, samplelist)
values = [to_float(getattr(self, key)) for key in samplelist]
if len(values) < len(samplelist):
values += [None] * (len(samplelist) - len(values))
elif len(values) > len(samplelist):
values = values[:len(samplelist)]
if variancefiledata:
tt = variancefiledata.split()
variances = map(webqtlUtil.StringAsFloat, tt)
elif variancepastedata:
tt = variancepastedata.split()
variances = map(webqtlUtil.StringAsFloat, tt)
else:
variances = map(self.FormVarianceAsFloat, samplelist)
if len(variances) < len(samplelist):
variances += [None]*(len(samplelist) - len(variances))
elif len(variances) > len(samplelist):
variances = variances[:len(samplelist)]
if Nfiledata:
tt = string.split(Nfiledata)
nsamples = map(webqtlUtil.IntAsFloat, tt)
if len(nsamples) < len(samplelist):
nsamples += [None]*(len(samplelist) - len(nsamples))
else:
nsamples = map(self.FormNAsFloat, samplelist)
##values, variances, nsamples is obsolete
self.allTraitData = {}
for i, _sample in enumerate(samplelist):
if values[i] != None:
self.allTraitData[_sample] = webqtlCaseData(
_sample, values[i], variances[i], nsamples[i])
def informativeStrains(self, samplelist=None, include_variances = None):
'''if readData was called, use this to output informative samples (sample with values)'''
if not samplelist:
samplelist = self.samplelist
samples = []
values = []
variances = []
for sample in samplelist:
if sample in self.allTraitData:
_val, _var = self.allTraitData[sample].value, self.allTraitData[sample].variance
if _val != None:
if include_variances:
if _var != None:
samples.append(sample)
values.append(_val)
variances.append(_var)
else:
samples.append(sample)
values.append(_val)
variances.append(None)
return samples, values, variances, len(samples)
def FormVarianceAsFloat(self, key):
try:
return float(self.formdata.getfirst('V' + key))
except:
return None
def FormNAsFloat(self, key):
try:
return int(self.formdata.getfirst('N' + key))
except:
return None
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