diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/webqtlFormData.py | 257 |
1 files changed, 0 insertions, 257 deletions
diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py deleted file mode 100644 index 1b41b2fc..00000000 --- a/wqflask/base/webqtlFormData.py +++ /dev/null @@ -1,257 +0,0 @@ -# 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 |