From 20be011f8b33fcde94037af19e403d3b76d5c9d1 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Fri, 13 Sep 2013 14:29:18 -0500 Subject: Added file that will convert genofiles to plink ped/map files --- wqflask/wqflask/my_pylmm/data/geno_to_ped.py | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 wqflask/wqflask/my_pylmm/data/geno_to_ped.py (limited to 'wqflask') diff --git a/wqflask/wqflask/my_pylmm/data/geno_to_ped.py b/wqflask/wqflask/my_pylmm/data/geno_to_ped.py new file mode 100644 index 00000000..9091ad9a --- /dev/null +++ b/wqflask/wqflask/my_pylmm/data/geno_to_ped.py @@ -0,0 +1,22 @@ +from __future__ import absolute_import, division, print_function + +import csv + +class ConvertToPed(object): + + def __init__(self, input_file, output_file): + self.input_file = input_file + self.output_file = output_file + + def convert(self): + + self.haplotype_notation = { + '@mat': "1", + '@pat': "0", + '@het': "0.5", + '@unk': "NA" + } + + with open(self.output_file, "w") as self.output_fh: + self.process_csv() + \ No newline at end of file -- cgit v1.2.3 From ce5d2b86af694c266cc0159be0438f187a058c20 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Tue, 24 Sep 2013 13:11:21 -0500 Subject: Fixed the db_tools import in mrna_assay_tissue_data.py Added file for the interval mapping page and wrote code that gets/sets some parameters --- wqflask/base/mrna_assay_tissue_data.py | 4 +- .../wqflask/interval_mapping/interval_mapping.py | 307 +++++++++++++++++++++ 2 files changed, 309 insertions(+), 2 deletions(-) create mode 100644 wqflask/wqflask/interval_mapping/interval_mapping.py (limited to 'wqflask') diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index 8ae71858..a08f3f21 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -4,8 +4,8 @@ import collections from flask import g -from utility import dbtools -from uitility import Bunch +from utility import db_tools +from utility import Bunch from MySQLdb import escape_string as escape diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py new file mode 100644 index 00000000..3ec08f6b --- /dev/null +++ b/wqflask/wqflask/interval_mapping/interval_mapping.py @@ -0,0 +1,307 @@ +from __future__ import absolute_import, print_function, division + +from base.trait import GeneralTrait +from base import data_set #import create_dataset + +from pprint import pformat as pf + +import string +import sys +import os +import collections + +import numpy as np +from scipy import linalg + +import simplejson as json + +#from redis import Redis + + +from base.trait import GeneralTrait +from base import data_set +from base import species +from base import webqtlConfig +from wqflask.my_pylmm.data import prep_data +from wqflask.my_pylmm.pyLMM import lmm +from wqflask.my_pylmm.pyLMM import input +from utility import helper_functions +from utility import Plot, Bunch +from utility import temp_data + +from utility.benchmark import Bench + + +class IntervalMapping(object): + + def __init__(self, start_vars, temp_uuid): + + #Currently only getting trait data for one trait, but will need + #to change this to accept multiple traits once the collection page is implemented + helper_functions.get_species_dataset_trait(self, start_vars) + + tempdata = temp_data.TempData(temp_uuid) + + self.samples = [] # Want only ones with values + self.vals = [] + + for sample in self.dataset.group.samplelist: + value = start_vars['value:' + sample] + self.samples.append(str(sample)) + self.vals.append(value) + + self.set_options(start_vars) + + self.gen_data(tempdata) + + #Get chromosome lengths for drawing the interval map plot + chromosome_mb_lengths = {} + for key in self.species.chromosomes.chromosomes.keys(): + chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length + + self.js_data = dict( + chromosomes = chromosome_mb_lengths, + qtl_results = self.qtl_results, + ) + + def get_qtl_results(self): + """Gets the LOD (or LRS) score at each marker in order do the qtl mapping""" + + + #INTERCROSS = (self.genotype.type=="intercross") + + #THESE ARE OLD COMMENTS + #draw the LRS scale + #We first determine whether or not we are using a sliding scale. + #If so, we need to compute the maximum LRS value to determine where the max y-value should be, and call this LRSMax. + #LRSTop is then defined to be above the LRSMax by enough to add one additional LRSScale increment. + #if we are using a set-scale, then we set LRSTop to be the user's value, and LRSMax doesn't matter. + + #if self.lrs_lod == 'LOD': + # lodm = self.LODFACTOR + #else: + # lodm = 1.0 + + if self.lrsMax <= 0: #sliding scale + LRSMax = max(map(max, self.qtlresults)).lrs + #genotype trait will give infinite LRS + LRSMax = min(LRSMax, webqtlConfig.MAXLRS) + if self.permChecked and not self.multipleInterval: + self.significance = min(self.significance, webqtlConfig.MAXLRS) + self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS) + LRSMax = max(self.significance, LRSMax) + else: + LRSMax = self.lrsMax*lodm + + if LRSMax/lodm > 100: + LRSScale = 20.0 + elif LRSMax/lodm > 20: + LRSScale = 5.0 + elif LRSMax/lodm > 7.5: + LRSScale = 2.5 + else: + LRSScale = 1.0 + + LRSAxisList = Plot.frange(LRSScale, LRSMax/lodm, LRSScale) + #make sure the user's value appears on the y-axis + #update by NL 6-21-2011: round the LOD value to 100 when LRSMax is equal to 460 + LRSAxisList.append(round(LRSMax/lodm)) + + #draw the "LRS" or "LOD" string to the left of the axis + LRSScaleFont=pid.Font(ttf="verdana", size=14*fontZoom, bold=0) + LRSLODFont=pid.Font(ttf="verdana", size=14*zoom*1.5, bold=0) + yZero = yTopOffset + plotHeight + + + canvas.drawString(self.LRS_LOD, xLeftOffset - canvas.stringWidth("999.99", font=LRSScaleFont) - 10*zoom, \ + yZero - 150, font=LRSLODFont, color=pid.black, angle=90) + + for item in LRSAxisList: + yLRS = yZero - (item*lodm/LRSMax) * LRSHeightThresh + canvas.drawLine(xLeftOffset, yLRS, xLeftOffset - 4, yLRS, color=self.LRS_COLOR, width=1*zoom) + scaleStr = "%2.1f" % item + canvas.drawString(scaleStr, xLeftOffset-4-canvas.stringWidth(scaleStr, font=LRSScaleFont)-5, yLRS+3, font=LRSScaleFont, color=self.LRS_COLOR) + + + #"Significant" and "Suggestive" Drawing Routine + # ======= Draw the thick lines for "Significant" and "Suggestive" ===== (crowell: I tried to make the SNPs draw over these lines, but piddle wouldn't have it...) + if self.permChecked and not self.multipleInterval: + significantY = yZero - self.significance*LRSHeightThresh/LRSMax + suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRSMax + startPosX = xLeftOffset + for i, _chr in enumerate(self.genotype): + rightEdge = int(startPosX + self.ChrLengthDistList[i]*plotXScale - self.SUGGESTIVE_WIDTH/1.5) + canvas.drawLine(startPosX+self.SUGGESTIVE_WIDTH/1.5, suggestiveY, rightEdge, suggestiveY, color=self.SUGGESTIVE_COLOR, + width=self.SUGGESTIVE_WIDTH*zoom, clipX=(xLeftOffset, xLeftOffset + plotWidth-2)) + canvas.drawLine(startPosX+self.SUGGESTIVE_WIDTH/1.5, significantY, rightEdge, significantY, color=self.SIGNIFICANT_COLOR, + width=self.SIGNIFICANT_WIDTH*zoom, clipX=(xLeftOffset, xLeftOffset + plotWidth-2)) + sugg_coords = "%d, %d, %d, %d" % (startPosX, suggestiveY-2, rightEdge + 2*zoom, suggestiveY+2) + sig_coords = "%d, %d, %d, %d" % (startPosX, significantY-2, rightEdge + 2*zoom, significantY+2) + if self.LRS_LOD == 'LRS': + sugg_title = "Suggestive LRS = %0.2f" % self.suggestive + sig_title = "Significant LRS = %0.2f" % self.significance + else: + sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive/4.61) + sig_title = "Significant LOD = %0.2f" % (self.significance/4.61) + Areas1 = HT.Area(shape='rect',coords=sugg_coords,title=sugg_title) + Areas2 = HT.Area(shape='rect',coords=sig_coords,title=sig_title) + gifmap.areas.append(Areas1) + gifmap.areas.append(Areas2) + + startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale + + + if self.multipleInterval: + lrsEdgeWidth = 1 + else: + additiveMax = max(map(lambda X : abs(X.additive), self.qtlresults[0])) + if INTERCROSS: + dominanceMax = max(map(lambda X : abs(X.dominance), self.qtlresults[0])) + else: + dominanceMax = -1 + lrsEdgeWidth = 2 + for i, qtlresult in enumerate(self.qtlresults): + m = 0 + startPosX = xLeftOffset + thisLRSColor = self.colorCollection[i] + for j, _chr in enumerate(self.genotype): + LRSCoordXY = [] + AdditiveCoordXY = [] + DominanceCoordXY = [] + for k, _locus in enumerate(_chr): + if self.plotScale == 'physic': + Xc = startPosX + (_locus.Mb-startMb)*plotXScale + else: + Xc = startPosX + (_locus.cM-_chr[0].cM)*plotXScale + # updated by NL 06-18-2011: + # fix the over limit LRS graph issue since genotype trait may give infinite LRS; + # for any lrs is over than 460(LRS max in this system), it will be reset to 460 + if qtlresult[m].lrs> 460 or qtlresult[m].lrs=='inf': + Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSMax + else: + Yc = yZero - qtlresult[m].lrs*LRSHeightThresh/LRSMax + + LRSCoordXY.append((Xc, Yc)) + if not self.multipleInterval and self.additiveChecked: + Yc = yZero - qtlresult[m].additive*AdditiveHeightThresh/additiveMax + AdditiveCoordXY.append((Xc, Yc)) + if not self.multipleInterval and INTERCROSS and self.additiveChecked: + Yc = yZero - qtlresult[m].dominance*DominanceHeightThresh/dominanceMax + DominanceCoordXY.append((Xc, Yc)) + m += 1 + canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + if not self.multipleInterval and self.additiveChecked: + plusColor = self.ADDITIVE_COLOR_POSITIVE + minusColor = self.ADDITIVE_COLOR_NEGATIVE + for k, aPoint in enumerate(AdditiveCoordXY): + if k > 0: + Xc0, Yc0 = AdditiveCoordXY[k-1] + Xc, Yc = aPoint + if (Yc0-yZero)*(Yc-yZero) < 0: + if Xc == Xc0: #genotype , locus distance is 0 + Xcm = Xc + else: + Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0 + if Yc0 < yZero: + canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + elif (Yc0-yZero)*(Yc-yZero) > 0: + if Yc < yZero: + canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + minYc = min(Yc-yZero, Yc0-yZero) + if minYc < 0: + canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + if not self.multipleInterval and INTERCROSS and self.dominanceChecked: + plusColor = self.DOMINANCE_COLOR_POSITIVE + minusColor = self.DOMINANCE_COLOR_NEGATIVE + for k, aPoint in enumerate(DominanceCoordXY): + if k > 0: + Xc0, Yc0 = DominanceCoordXY[k-1] + Xc, Yc = aPoint + if (Yc0-yZero)*(Yc-yZero) < 0: + if Xc == Xc0: #genotype , locus distance is 0 + Xcm = Xc + else: + Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0 + if Yc0 < yZero: + canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + elif (Yc0-yZero)*(Yc-yZero) > 0: + if Yc < yZero: + canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + minYc = min(Yc-yZero, Yc0-yZero) + if minYc < 0: + canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale + + ###draw additive scale + if not self.multipleInterval and self.additiveChecked: + additiveScaleFont=pid.Font(ttf="verdana",size=12*fontZoom,bold=0) + additiveScale = Plot.detScaleOld(0,additiveMax) + additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2] + additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep) + maxAdd = additiveScale[1] + addPlotScale = AdditiveHeightThresh/additiveMax + + additiveAxisList.append(additiveScale[1]) + for item in additiveAxisList: + additiveY = yZero - item*addPlotScale + canvas.drawLine(xLeftOffset + plotWidth,additiveY,xLeftOffset+4+ plotWidth,additiveY,color=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom) + scaleStr = "%2.3f" % item + canvas.drawString(scaleStr,xLeftOffset + plotWidth +6,additiveY+5,font=additiveScaleFont,color=self.ADDITIVE_COLOR_POSITIVE) + + canvas.drawLine(xLeftOffset+plotWidth,additiveY,xLeftOffset+plotWidth,yZero,color=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom) + + canvas.drawLine(xLeftOffset, yZero, xLeftOffset, yTopOffset, color=self.LRS_COLOR, width=1*zoom) #the blue line running up the y axis + + + def set_options(self, start_vars): + """Sets various options (physical/genetic mapping, # permutations, which chromosome""" + + self.plot_scale = start_vars['scale'] + #if self.plotScale == 'physic' and not fd.genotype.Mbmap: + # self.plotScale = 'morgan' + self.num_permutations = start_vars['num_permutations'] + self.do_bootstrap = start_vars['do_bootstrap'] + self.control_locus = start_vars['control_locus'] + self.selected_chr = start_vars['selected_chr'] + + + def identify_empty_samples(self): + no_val_samples = [] + for sample_count, val in enumerate(self.vals): + if val == "x": + no_val_samples.append(sample_count) + return no_val_samples + + def trim_genotypes(self, genotype_data, no_value_samples): + trimmed_genotype_data = [] + for marker in genotype_data: + new_genotypes = [] + for item_count, genotype in enumerate(marker): + if item_count in no_value_samples: + continue + try: + genotype = float(genotype) + except ValueError: + genotype = np.nan + pass + new_genotypes.append(genotype) + trimmed_genotype_data.append(new_genotypes) + return trimmed_genotype_data \ No newline at end of file -- cgit v1.2.3 From 4c37e3962d6f34a935ea23511e5b760be4208474 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Tue, 24 Sep 2013 14:25:28 -0500 Subject: Just committing a few additions to the interval mapping code --- web/webqtl/intervalMapping/IntervalMappingPage.py | 2 +- .../wqflask/interval_mapping/interval_mapping.py | 370 +++++++++------------ 2 files changed, 162 insertions(+), 210 deletions(-) (limited to 'wqflask') diff --git a/web/webqtl/intervalMapping/IntervalMappingPage.py b/web/webqtl/intervalMapping/IntervalMappingPage.py index 4bdf45ab..c3ef1cbd 100755 --- a/web/webqtl/intervalMapping/IntervalMappingPage.py +++ b/web/webqtl/intervalMapping/IntervalMappingPage.py @@ -2038,7 +2038,7 @@ class IntervalMappingPage(templatePage): qtlresult = self.genotype.regression(strains = _strains, trait = _vals) self.qtlresults.append(qtlresult) - + if not self.multipleInterval: if self.controlLocus and self.selectedChr > -1: self.genotype.chromosome = [self.genotype[self.selectedChr]] diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py index 3ec08f6b..48e8018e 100644 --- a/wqflask/wqflask/interval_mapping/interval_mapping.py +++ b/wqflask/wqflask/interval_mapping/interval_mapping.py @@ -52,7 +52,7 @@ class IntervalMapping(object): self.set_options(start_vars) - self.gen_data(tempdata) + self.gen_qtl_results(tempdata) #Get chromosome lengths for drawing the interval map plot chromosome_mb_lengths = {} @@ -60,217 +60,11 @@ class IntervalMapping(object): chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length self.js_data = dict( + lrs_lod = self.lrs_lod, chromosomes = chromosome_mb_lengths, qtl_results = self.qtl_results, ) - def get_qtl_results(self): - """Gets the LOD (or LRS) score at each marker in order do the qtl mapping""" - - - #INTERCROSS = (self.genotype.type=="intercross") - - #THESE ARE OLD COMMENTS - #draw the LRS scale - #We first determine whether or not we are using a sliding scale. - #If so, we need to compute the maximum LRS value to determine where the max y-value should be, and call this LRSMax. - #LRSTop is then defined to be above the LRSMax by enough to add one additional LRSScale increment. - #if we are using a set-scale, then we set LRSTop to be the user's value, and LRSMax doesn't matter. - - #if self.lrs_lod == 'LOD': - # lodm = self.LODFACTOR - #else: - # lodm = 1.0 - - if self.lrsMax <= 0: #sliding scale - LRSMax = max(map(max, self.qtlresults)).lrs - #genotype trait will give infinite LRS - LRSMax = min(LRSMax, webqtlConfig.MAXLRS) - if self.permChecked and not self.multipleInterval: - self.significance = min(self.significance, webqtlConfig.MAXLRS) - self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS) - LRSMax = max(self.significance, LRSMax) - else: - LRSMax = self.lrsMax*lodm - - if LRSMax/lodm > 100: - LRSScale = 20.0 - elif LRSMax/lodm > 20: - LRSScale = 5.0 - elif LRSMax/lodm > 7.5: - LRSScale = 2.5 - else: - LRSScale = 1.0 - - LRSAxisList = Plot.frange(LRSScale, LRSMax/lodm, LRSScale) - #make sure the user's value appears on the y-axis - #update by NL 6-21-2011: round the LOD value to 100 when LRSMax is equal to 460 - LRSAxisList.append(round(LRSMax/lodm)) - - #draw the "LRS" or "LOD" string to the left of the axis - LRSScaleFont=pid.Font(ttf="verdana", size=14*fontZoom, bold=0) - LRSLODFont=pid.Font(ttf="verdana", size=14*zoom*1.5, bold=0) - yZero = yTopOffset + plotHeight - - - canvas.drawString(self.LRS_LOD, xLeftOffset - canvas.stringWidth("999.99", font=LRSScaleFont) - 10*zoom, \ - yZero - 150, font=LRSLODFont, color=pid.black, angle=90) - - for item in LRSAxisList: - yLRS = yZero - (item*lodm/LRSMax) * LRSHeightThresh - canvas.drawLine(xLeftOffset, yLRS, xLeftOffset - 4, yLRS, color=self.LRS_COLOR, width=1*zoom) - scaleStr = "%2.1f" % item - canvas.drawString(scaleStr, xLeftOffset-4-canvas.stringWidth(scaleStr, font=LRSScaleFont)-5, yLRS+3, font=LRSScaleFont, color=self.LRS_COLOR) - - - #"Significant" and "Suggestive" Drawing Routine - # ======= Draw the thick lines for "Significant" and "Suggestive" ===== (crowell: I tried to make the SNPs draw over these lines, but piddle wouldn't have it...) - if self.permChecked and not self.multipleInterval: - significantY = yZero - self.significance*LRSHeightThresh/LRSMax - suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRSMax - startPosX = xLeftOffset - for i, _chr in enumerate(self.genotype): - rightEdge = int(startPosX + self.ChrLengthDistList[i]*plotXScale - self.SUGGESTIVE_WIDTH/1.5) - canvas.drawLine(startPosX+self.SUGGESTIVE_WIDTH/1.5, suggestiveY, rightEdge, suggestiveY, color=self.SUGGESTIVE_COLOR, - width=self.SUGGESTIVE_WIDTH*zoom, clipX=(xLeftOffset, xLeftOffset + plotWidth-2)) - canvas.drawLine(startPosX+self.SUGGESTIVE_WIDTH/1.5, significantY, rightEdge, significantY, color=self.SIGNIFICANT_COLOR, - width=self.SIGNIFICANT_WIDTH*zoom, clipX=(xLeftOffset, xLeftOffset + plotWidth-2)) - sugg_coords = "%d, %d, %d, %d" % (startPosX, suggestiveY-2, rightEdge + 2*zoom, suggestiveY+2) - sig_coords = "%d, %d, %d, %d" % (startPosX, significantY-2, rightEdge + 2*zoom, significantY+2) - if self.LRS_LOD == 'LRS': - sugg_title = "Suggestive LRS = %0.2f" % self.suggestive - sig_title = "Significant LRS = %0.2f" % self.significance - else: - sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive/4.61) - sig_title = "Significant LOD = %0.2f" % (self.significance/4.61) - Areas1 = HT.Area(shape='rect',coords=sugg_coords,title=sugg_title) - Areas2 = HT.Area(shape='rect',coords=sig_coords,title=sig_title) - gifmap.areas.append(Areas1) - gifmap.areas.append(Areas2) - - startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale - - - if self.multipleInterval: - lrsEdgeWidth = 1 - else: - additiveMax = max(map(lambda X : abs(X.additive), self.qtlresults[0])) - if INTERCROSS: - dominanceMax = max(map(lambda X : abs(X.dominance), self.qtlresults[0])) - else: - dominanceMax = -1 - lrsEdgeWidth = 2 - for i, qtlresult in enumerate(self.qtlresults): - m = 0 - startPosX = xLeftOffset - thisLRSColor = self.colorCollection[i] - for j, _chr in enumerate(self.genotype): - LRSCoordXY = [] - AdditiveCoordXY = [] - DominanceCoordXY = [] - for k, _locus in enumerate(_chr): - if self.plotScale == 'physic': - Xc = startPosX + (_locus.Mb-startMb)*plotXScale - else: - Xc = startPosX + (_locus.cM-_chr[0].cM)*plotXScale - # updated by NL 06-18-2011: - # fix the over limit LRS graph issue since genotype trait may give infinite LRS; - # for any lrs is over than 460(LRS max in this system), it will be reset to 460 - if qtlresult[m].lrs> 460 or qtlresult[m].lrs=='inf': - Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSMax - else: - Yc = yZero - qtlresult[m].lrs*LRSHeightThresh/LRSMax - - LRSCoordXY.append((Xc, Yc)) - if not self.multipleInterval and self.additiveChecked: - Yc = yZero - qtlresult[m].additive*AdditiveHeightThresh/additiveMax - AdditiveCoordXY.append((Xc, Yc)) - if not self.multipleInterval and INTERCROSS and self.additiveChecked: - Yc = yZero - qtlresult[m].dominance*DominanceHeightThresh/dominanceMax - DominanceCoordXY.append((Xc, Yc)) - m += 1 - canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - if not self.multipleInterval and self.additiveChecked: - plusColor = self.ADDITIVE_COLOR_POSITIVE - minusColor = self.ADDITIVE_COLOR_NEGATIVE - for k, aPoint in enumerate(AdditiveCoordXY): - if k > 0: - Xc0, Yc0 = AdditiveCoordXY[k-1] - Xc, Yc = aPoint - if (Yc0-yZero)*(Yc-yZero) < 0: - if Xc == Xc0: #genotype , locus distance is 0 - Xcm = Xc - else: - Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0 - if Yc0 < yZero: - canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - else: - canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - elif (Yc0-yZero)*(Yc-yZero) > 0: - if Yc < yZero: - canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - else: - canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - else: - minYc = min(Yc-yZero, Yc0-yZero) - if minYc < 0: - canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - else: - canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - if not self.multipleInterval and INTERCROSS and self.dominanceChecked: - plusColor = self.DOMINANCE_COLOR_POSITIVE - minusColor = self.DOMINANCE_COLOR_NEGATIVE - for k, aPoint in enumerate(DominanceCoordXY): - if k > 0: - Xc0, Yc0 = DominanceCoordXY[k-1] - Xc, Yc = aPoint - if (Yc0-yZero)*(Yc-yZero) < 0: - if Xc == Xc0: #genotype , locus distance is 0 - Xcm = Xc - else: - Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0 - if Yc0 < yZero: - canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - else: - canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - elif (Yc0-yZero)*(Yc-yZero) > 0: - if Yc < yZero: - canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - else: - canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - else: - minYc = min(Yc-yZero, Yc0-yZero) - if minYc < 0: - canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - else: - canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=1, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale - - ###draw additive scale - if not self.multipleInterval and self.additiveChecked: - additiveScaleFont=pid.Font(ttf="verdana",size=12*fontZoom,bold=0) - additiveScale = Plot.detScaleOld(0,additiveMax) - additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2] - additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep) - maxAdd = additiveScale[1] - addPlotScale = AdditiveHeightThresh/additiveMax - - additiveAxisList.append(additiveScale[1]) - for item in additiveAxisList: - additiveY = yZero - item*addPlotScale - canvas.drawLine(xLeftOffset + plotWidth,additiveY,xLeftOffset+4+ plotWidth,additiveY,color=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom) - scaleStr = "%2.3f" % item - canvas.drawString(scaleStr,xLeftOffset + plotWidth +6,additiveY+5,font=additiveScaleFont,color=self.ADDITIVE_COLOR_POSITIVE) - - canvas.drawLine(xLeftOffset+plotWidth,additiveY,xLeftOffset+plotWidth,yZero,color=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom) - - canvas.drawLine(xLeftOffset, yZero, xLeftOffset, yTopOffset, color=self.LRS_COLOR, width=1*zoom) #the blue line running up the y axis - - def set_options(self, start_vars): """Sets various options (physical/genetic mapping, # permutations, which chromosome""" @@ -281,6 +75,38 @@ class IntervalMapping(object): self.do_bootstrap = start_vars['do_bootstrap'] self.control_locus = start_vars['control_locus'] self.selected_chr = start_vars['selected_chr'] + self.weighted_regression = start_vars['weighted'] + self.lrs_lod = start_vars['lrs_lod'] + + + def gen_qtl_results(self, tempdata): + """Generates qtl results for plotting interval map""" + + self.dataset.group.get_markers() + + pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals]) + + #if self.dataset.group.species == "human": + # p_values, t_stats = self.gen_human_results(pheno_vector, tempdata) + #else: + genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers] + + no_val_samples = self.identify_empty_samples() + trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples) + + genotype_matrix = np.array(trimmed_genotype_data).T + + t_stats, p_values = lmm.run( + pheno_vector, + genotype_matrix, + restricted_max_likelihood=True, + refit=False, + temp_data=tempdata + ) + + self.dataset.group.markers.add_pvalues(p_values) + + self.qtl_results = self.dataset.group.markers.markers def identify_empty_samples(self): @@ -290,6 +116,7 @@ class IntervalMapping(object): no_val_samples.append(sample_count) return no_val_samples + def trim_genotypes(self, genotype_data, no_value_samples): trimmed_genotype_data = [] for marker in genotype_data: @@ -304,4 +131,129 @@ class IntervalMapping(object): pass new_genotypes.append(genotype) trimmed_genotype_data.append(new_genotypes) - return trimmed_genotype_data \ No newline at end of file + return trimmed_genotype_data + + #def get_qtl_results(self): + # """Gets the LOD (or LRS) score at each marker in order do the qtl mapping""" + # + # + # + # #self.genotype = self.genotype.addinterval() + # #resultSlice = [] + # #controlGeno = [] + # + # #if self.multipleInterval: + # # self.suggestive = 0 + # # self.significance = 0 + # # if self.selectedChr > -1: + # # self.genotype.chromosome = [self.genotype[self.selectedChr]] + # #else: + # #single interval mapping + # #try: + # # self.suggestive = float(fd.formdata.getvalue('permSuggestive')) + # # self.significance = float(fd.formdata.getvalue('permSignificance')) + # #except: + # # self.suggestive = None + # # self.significance = None + # + # #NOT DOING MULTIPLE TRAITS YET, BUT WILL NEED TO LATER + # #_strains, _vals, _vars = self.traitList[0].exportInformative(weightedRegression) + # + # #if webqtlUtil.ListNotNull(_vars): + # # pass + # #else: + # # weightedRegression = 0 + # # _strains, _vals, _vars = self.traitList[0].exportInformative() + # + # ##locate genotype of control Locus + # #if self.controlLocus: + # # controlGeno2 = [] + # # _FIND = 0 + # # for _chr in self.genotype: + # # for _locus in _chr: + # # if _locus.name == self.controlLocus: + # # controlGeno2 = _locus.genotype + # # _FIND = 1 + # # break + # # if _FIND: + # # break + # # if controlGeno2: + # # _prgy = list(self.genotype.prgy) + # # for _strain in _strains: + # # _idx = _prgy.index(_strain) + # # controlGeno.append(controlGeno2[_idx]) + # # else: + # # return "The control marker you selected is not in the genofile." + # # + # # + # # if self.significance and self.suggestive: + # # pass + # # else: + # # if self.permChecked: + # # if weightedRegression: + # # self.LRSArray = self.genotype.permutation(strains = _strains, trait = _vals, + # # variance = _vars, nperm=fd.nperm) + # # else: + # # self.LRSArray = self.genotype.permutation(strains = _strains, trait = _vals, + # # nperm=fd.nperm) + # # self.suggestive = self.LRSArray[int(fd.nperm*0.37-1)] + # # self.significance = self.LRSArray[int(fd.nperm*0.95-1)] + # # + # # else: + # # self.suggestive = 9.2 + # # self.significance = 16.1 + # # + # # #calculating bootstrap + # # #from now on, genotype could only contain a single chromosome + # # #permutation need to be performed genome wide, this is not the case for bootstrap + # # + # # #due to the design of qtlreaper, composite regression need to be performed genome wide + # # if not self.controlLocus and self.selectedChr > -1: + # # self.genotype.chromosome = [self.genotype[self.selectedChr]] + # # elif self.selectedChr > -1: #self.controlLocus and self.selectedChr > -1 + # # lociPerChr = map(len, self.genotype) + # # resultSlice = reduce(lambda X, Y: X+Y, lociPerChr[:self.selectedChr], 0) + # # resultSlice = [resultSlice,resultSlice+lociPerChr[self.selectedChr]] + # # else: + # # pass + # + # #calculate QTL for each trait + # self.qtl_results = [] + # + # #for thisTrait in self.traitList: + # _strains, _vals, _vars = thisTrait.exportInformative(weightedRegression) + # if self.controlLocus: + # if weightedRegression: + # qtlresult = self.genotype.regression(strains = _strains, trait = _vals, + # variance = _vars, control = self.controlLocus) + # else: + # qtlresult = self.genotype.regression(strains = _strains, trait = _vals, + # control = self.controlLocus) + # if resultSlice: + # qtlresult = qtlresult[resultSlice[0]:resultSlice[1]] + # else: + # if weightedRegression: + # qtlresult = self.genotype.regression(strains = _strains, trait = _vals, + # variance = _vars) + # else: + # qtlresult = self.genotype.regression(strains = _strains, trait = _vals) + # + # self.qtlresults.append(qtlresult) + # + # if not self.multipleInterval: + # if self.controlLocus and self.selectedChr > -1: + # self.genotype.chromosome = [self.genotype[self.selectedChr]] + # + # if self.bootChecked: + # if controlGeno: + # self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals, + # control = controlGeno, nboot=fd.nboot) + # elif weightedRegression: + # self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals, + # variance = _vars, nboot=fd.nboot) + # else: + # self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals, + # nboot=fd.nboot) + # else: + # self.bootResult = [] + -- cgit v1.2.3 From 3325184b1dd310619626dd31852ab84cae6dc7fc Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Tue, 8 Oct 2013 12:13:56 -0500 Subject: Did some work with interval mapping page; will use qtl reaper to do the mapping, since it is reliable/fast and avoids us having to rewrite from scratch using something like r/qtl --- wqflask/base/data_set.py | 20 ++++---- wqflask/maintenance/quick_search_table.py | 4 +- .../wqflask/interval_mapping/interval_mapping.py | 53 ++++++++++++++++++++++ 3 files changed, 67 insertions(+), 10 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 96e04df0..befbd518 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -168,13 +168,13 @@ class Markers(object): for marker, p_value in itertools.izip(self.markers, p_values): marker['p_value'] = p_value - if marker['p_value'] == 0: - marker['lod_score'] = 0 - marker['lrs_value'] = 0 - else: - 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 + if math.isnan(marker['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): @@ -189,6 +189,8 @@ class HumanMarkers(Markers): 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): @@ -315,10 +317,10 @@ class DatasetGroup(object): #determine default genotype object if self.incparentsf1 and genotype_1.type != "intercross": - genotype = genotype_2 + self.genotype = genotype_2 else: self.incparentsf1 = 0 - genotype = genotype_1 + self.genotype = genotype_1 self.samplelist = list(genotype.prgy) diff --git a/wqflask/maintenance/quick_search_table.py b/wqflask/maintenance/quick_search_table.py index 9cd792ef..23bd505c 100644 --- a/wqflask/maintenance/quick_search_table.py +++ b/wqflask/maintenance/quick_search_table.py @@ -11,8 +11,10 @@ each trait, its dataset, and several columns determined by its trait type (pheno """ -from __future__ import print_function, division, absolute_import +from __future__ import absolute_import, division, print_function +# We do this here so we can use zach_settings +# Not to avoid other absoulte_imports import sys sys.path.append("../../..") diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py index 48e8018e..5d660224 100644 --- a/wqflask/wqflask/interval_mapping/interval_mapping.py +++ b/wqflask/wqflask/interval_mapping/interval_mapping.py @@ -12,6 +12,7 @@ import collections import numpy as np from scipy import linalg +import rpy2.robjects import simplejson as json @@ -83,6 +84,28 @@ class IntervalMapping(object): """Generates qtl results for plotting interval map""" self.dataset.group.get_markers() + self.dataset.read_genotype_file() + + samples, values, variances = self.trait.export_informative() + if self.control_locus: + if self.weighted_regression: + qtl_result = self.dataset.genotype.regression(strains = samples, + trait = values, + variance = variances, + control = self.control_locus) + else: + qtl_result = self.dataset.genotype.regression(strains = samples, + trait = values, + control = self.control_locus) + else: + if self.weighted_regression: + qtl_result = self.dataset.genotype.regression(strains = samples, + trait = values, + variance = variances) + else: + qtl_result = self.dataset.genotype.regression(strains = samples, + trait = values) + pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals]) @@ -108,6 +131,36 @@ class IntervalMapping(object): self.qtl_results = self.dataset.group.markers.markers + #def gen_qtl_results_2(self, tempdata): + # """Generates qtl results for plotting interval map""" + # + # self.dataset.group.get_markers() + # self.dataset.read_genotype_file() + # + # pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals]) + # + # #if self.dataset.group.species == "human": + # # p_values, t_stats = self.gen_human_results(pheno_vector, tempdata) + # #else: + # genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers] + # + # no_val_samples = self.identify_empty_samples() + # trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples) + # + # genotype_matrix = np.array(trimmed_genotype_data).T + # + # t_stats, p_values = lmm.run( + # pheno_vector, + # genotype_matrix, + # restricted_max_likelihood=True, + # refit=False, + # temp_data=tempdata + # ) + # + # self.dataset.group.markers.add_pvalues(p_values) + # + # self.qtl_results = self.dataset.group.markers.markers + def identify_empty_samples(self): no_val_samples = [] -- cgit v1.2.3 From a823e66f8dc742e1608b3e0db6d521d5f63b641a Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Tue, 15 Oct 2013 15:06:36 -0500 Subject: Changed templates to call the header macro Correlation page now works with Non-BXD (or whatever group) or All Samples options --- wqflask/base/data_set.py | 14 ++++++++------ wqflask/wqflask/correlation/show_corr_results.py | 4 ++-- wqflask/wqflask/templates/base.html | 4 ++-- wqflask/wqflask/templates/correlation_page.html | 8 ++------ wqflask/wqflask/templates/index_page.html | 2 -- wqflask/wqflask/templates/marker_regression.html | 10 ++-------- wqflask/wqflask/templates/quick_search.html | 11 +++-------- wqflask/wqflask/templates/search_result_page.html | 10 ++-------- wqflask/wqflask/templates/show_trait.html | 11 +++-------- 9 files changed, 24 insertions(+), 50 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 9fa7beb3..f25e7974 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -322,7 +322,7 @@ class DatasetGroup(object): self.incparentsf1 = 0 self.genotype = genotype_1 - self.samplelist = list(genotype.prgy) + self.samplelist = list(self.genotype.prgy) #class DataSets(object): @@ -440,10 +440,12 @@ class DataSet(object): def get_trait_data(self, sample_list=None): if sample_list: - self.samplelist = sample_list + self.group.parlist + self.group.f1list + self.samplelist = sample_list else: - self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list - + self.samplelist = self.group.samplelist + + if (self.group.parlist + self.group.f1list) in self.samplelist: + self.samplelist += self.group.parlist + self.group.f1list query = """ SELECT Strain.Name, Strain.Id FROM Strain, Species @@ -503,8 +505,8 @@ class DataSet(object): and {}Freeze.Name = '{}' and {}.Id = {}XRef.{}Id order by {}.Id - """.format(*mescape(self.type, self.type, self.type, self.type, - self.name, dataset_type, self.type, self.type, dataset_type)) + """.format(*mescape(self.type, self.type, self.type, self.name, + dataset_type, self.type, dataset_type, dataset_type)) else: query += """ WHERE {}XRef.{}FreezeId = {}Freeze.Id diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index a5c80674..8f23165c 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -178,10 +178,10 @@ class CorrelationResults(object): trait_object.lit_corr = lit_corr_data[trait][1] self.correlation_results.append(trait_object) - if self.corr_type != "lit": + if self.corr_type != "lit" and self.dataset.type == "ProbeSet": self.do_lit_correlation_for_trait_list() - if self.corr_type != "tissue": + if self.corr_type != "tissue" and self.dataset.type == "ProbeSet": self.do_tissue_correlation_for_trait_list() #print("self.correlation_results: ", pf(self.correlation_results)) diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index 8efba6a7..a14eeb44 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -29,9 +29,9 @@ {% macro header(main, second) %}
-

Login

+

{{ main }}

- Gain access to GeneNetwork. + {{ second }}

diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index 4d09cf20..7e149506 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -6,12 +6,8 @@ {% endblock %} {% block content %} - -
-
-

Correlation

-
-
+ + {{ header("Correlation", 'Trait: {} Dataset: {}'.format(this_trait.name, dataset.name)) }} diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html index 98682e57..d177a7bd 100644 --- a/wqflask/wqflask/templates/index_page.html +++ b/wqflask/wqflask/templates/index_page.html @@ -3,8 +3,6 @@ {% block content %} - -

GeneNetwork

diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html index 9260acab..64d2e9b7 100644 --- a/wqflask/wqflask/templates/marker_regression.html +++ b/wqflask/wqflask/templates/marker_regression.html @@ -9,14 +9,8 @@ {% endblock %} {% block content %} -
-
-

Marker Regression

-

- {{ this_trait.name }}: {{ this_trait.description_fmt }} -

-
-
+ {{ header("Marker Regression", + '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
diff --git a/wqflask/wqflask/templates/quick_search.html b/wqflask/wqflask/templates/quick_search.html index b0e38708..2f268c5a 100644 --- a/wqflask/wqflask/templates/quick_search.html +++ b/wqflask/wqflask/templates/quick_search.html @@ -2,14 +2,9 @@ {% block title %}QuickSearch Results{% endblock %} {% block content %} -
-
-

QuickSearch Results

-

- GeneNetwork found {{ numify(results|count, "record", "records") }}. -

-
-
+ + {{ header("QuickSearch Results", + 'GeneNetwork found {}.'.format(numify(results|count, "record", "records"))) }}
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 11f68bba..1fe7cce9 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -2,14 +2,8 @@ {% block title %}Search Results{% endblock %} {% block content %} -
-
-

Search Results

-

- GeneNetwork found {{ numify(results|count, "record", "records") }}. -

-
-
+ {{ header("Search Results", + 'GeneNetwork found {}.'.format(numify(results|count, "record", "records"))) }}
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 799245c3..e3c84de7 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -7,14 +7,9 @@ {% endblock %} {% block content %} -
-
-

{{ this_trait.symbol}}

-

- {{ this_trait.name }}: {{ this_trait.description_fmt }} -

-
-
+ {{ header("{}".format(this_trait.symbol), + '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }} +
-- cgit v1.2.3 From da0526b9d870ba937fcf860c40731c9d96eb9f63 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Wed, 16 Oct 2013 18:02:28 -0500 Subject: Added interval_mapping to views.py Made some more changes to interval_mapping.py --- misc/notes.txt | 3 + .../wqflask/interval_mapping/interval_mapping.py | 70 +++++++++++----------- wqflask/wqflask/views.py | 44 ++++++++++++++ 3 files changed, 82 insertions(+), 35 deletions(-) mode change 100644 => 100755 wqflask/wqflask/interval_mapping/interval_mapping.py (limited to 'wqflask') diff --git a/misc/notes.txt b/misc/notes.txt index 91a0e67c..f6a2bb33 100644 --- a/misc/notes.txt +++ b/misc/notes.txt @@ -90,6 +90,9 @@ Reload web server: Run server: python runserver.py +Run sendmail.py +python send_mail.py + =========================================== UFW - default firewall confirguation tool for Ubuntu; eases iptables firewall configuration diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py old mode 100644 new mode 100755 index 5d660224..aca99cbe --- a/wqflask/wqflask/interval_mapping/interval_mapping.py +++ b/wqflask/wqflask/interval_mapping/interval_mapping.py @@ -89,26 +89,56 @@ class IntervalMapping(object): samples, values, variances = self.trait.export_informative() if self.control_locus: if self.weighted_regression: - qtl_result = self.dataset.genotype.regression(strains = samples, + self.qtl_results = self.dataset.genotype.regression(strains = samples, trait = values, variance = variances, control = self.control_locus) else: - qtl_result = self.dataset.genotype.regression(strains = samples, + self.qtl_results = self.dataset.genotype.regression(strains = samples, trait = values, control = self.control_locus) else: if self.weighted_regression: - qtl_result = self.dataset.genotype.regression(strains = samples, + self.qtl_results = self.dataset.genotype.regression(strains = samples, trait = values, variance = variances) else: - qtl_result = self.dataset.genotype.regression(strains = samples, + self.qtl_results = self.dataset.genotype.regression(strains = samples, trait = values) - pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals]) + #pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals]) + + #if self.dataset.group.species == "human": + # p_values, t_stats = self.gen_human_results(pheno_vector, tempdata) + #else: + genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers] + + no_val_samples = self.identify_empty_samples() + trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples) + + genotype_matrix = np.array(trimmed_genotype_data).T + + #t_stats, p_values = lmm.run( + # pheno_vector, + # genotype_matrix, + # restricted_max_likelihood=True, + # refit=False, + # temp_data=tempdata + #) + + #self.dataset.group.markers.add_pvalues(p_values) + + #self.qtl_results = self.dataset.group.markers.markers + def gen_qtl_results_2(self, tempdata): + """Generates qtl results for plotting interval map""" + + self.dataset.group.get_markers() + self.dataset.read_genotype_file() + + pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals]) + #if self.dataset.group.species == "human": # p_values, t_stats = self.gen_human_results(pheno_vector, tempdata) #else: @@ -131,36 +161,6 @@ class IntervalMapping(object): self.qtl_results = self.dataset.group.markers.markers - #def gen_qtl_results_2(self, tempdata): - # """Generates qtl results for plotting interval map""" - # - # self.dataset.group.get_markers() - # self.dataset.read_genotype_file() - # - # pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals]) - # - # #if self.dataset.group.species == "human": - # # p_values, t_stats = self.gen_human_results(pheno_vector, tempdata) - # #else: - # genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers] - # - # no_val_samples = self.identify_empty_samples() - # trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples) - # - # genotype_matrix = np.array(trimmed_genotype_data).T - # - # t_stats, p_values = lmm.run( - # pheno_vector, - # genotype_matrix, - # restricted_max_likelihood=True, - # refit=False, - # temp_data=tempdata - # ) - # - # self.dataset.group.markers.add_pvalues(p_values) - # - # self.qtl_results = self.dataset.group.markers.markers - def identify_empty_samples(self): no_val_samples = [] diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index deccf459..29f7f150 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -32,6 +32,7 @@ from base.data_set import create_datasets_list from wqflask.show_trait import show_trait from wqflask.show_trait import export_trait_data from wqflask.marker_regression import marker_regression +from wqflask.interval_mapping import interval_mapping from wqflask.correlation import show_corr_results from utility import temp_data @@ -246,6 +247,49 @@ def marker_regression_page(): return rendered_template +@app.route("/interval_mapping", methods=('POST',)) +def interval_mapping_page(): + initial_start_vars = request.form + temp_uuid = initial_start_vars['temp_uuid'] + wanted = ( + 'trait_id', + 'dataset', + 'suggestive' + ) + + start_vars = {} + for key, value in initial_start_vars.iteritems(): + if key in wanted or key.startswith(('value:')): + start_vars[key] = value + + version = "v1" + key = "interval_mapping:{}:".format(version) + json.dumps(start_vars, sort_keys=True) + print("key is:", pf(key)) + with Bench("Loading cache"): + result = Redis.get(key) + + if result: + print("Cache hit!!!") + with Bench("Loading results"): + result = pickle.loads(result) + else: + print("Cache miss!!!") + template_vars = interval_mapping.IntervalMapping(start_vars, temp_uuid) + + template_vars.js_data = json.dumps(template_vars.js_data, + default=json_default_handler, + indent=" ") + + result = template_vars.__dict__ + + #causeerror + Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL)) + Redis.expire(key, 60*60) + + with Bench("Rendering template"): + rendered_template = render_template("interval_mapping.html", **result) + + return rendered_template @app.route("/corr_compute", methods=('POST',)) def corr_compute_page(): -- cgit v1.2.3