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-rw-r--r--wqflask/base/webqtlFormData.py257
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diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
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--- a/wqflask/base/webqtlFormData.py
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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 \ No newline at end of file
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 20:22:42 +0000