aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/base/mrna_assay_tissue_data.py4
-rw-r--r--wqflask/wqflask/interval_mapping/interval_mapping.py307
2 files changed, 309 insertions, 2 deletions
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
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 19:18:34 +0000