diff options
Diffstat (limited to 'wqflask/utility')
| -rw-r--r--[-rwxr-xr-x] | wqflask/utility/Plot.py | 353 | ||||
| -rw-r--r-- | wqflask/utility/external.py | 9 | ||||
| -rw-r--r-- | wqflask/utility/genofile_parser.py | 100 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 189 | ||||
| -rwxr-xr-x | wqflask/utility/webqtlUtil.py | 2 |
5 files changed, 407 insertions, 246 deletions
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 51a57a6d..444c71c9 100755..100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -24,10 +24,9 @@ # # Last updated by GeneNetwork Core Team 2010/10/20 -#import piddle as pid - from __future__ import print_function +import piddle as pid from pprint import pformat as pf print("Lysol") @@ -478,181 +477,181 @@ def plotSecurity(canvas, text="12345"): # parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py) # or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py) -#def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1): -# -# xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset -# -# plotWidth = canvas.size[0] - xLeftOffset - xRightOffset -# plotHeight = canvas.size[1] - yTopOffset - yBottomOffset -# if plotHeight<=0 or plotWidth<=0: -# return -# -# if len(data) < 2: -# return -# -# max_D = max(data) -# min_D = min(data) -# #add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong -# if max_D == float('inf') or max_D>webqtlConfig.MAXLRS: -# max_D=webqtlConfig.MAXLRS #maximum LRS value -# -# xLow, xTop, stepX = detScale(min_D, max_D) -# -# #reduce data -# step = ceil((xTop-xLow)/50.0) -# j = xLow -# dataXY = [] -# Count = [] -# while j <= xTop: -# dataXY.append(j) -# Count.append(0) -# j += step -# -# for i, item in enumerate(data): -# if item == float('inf') or item>webqtlConfig.MAXLRS: -# item = webqtlConfig.MAXLRS #maximum LRS value -# j = int((item-xLow)/step) -# Count[j] += 1 -# -# yLow, yTop, stepY=detScale(0,max(Count)) -# -# #draw data -# xScale = plotWidth/(xTop-xLow) -# yScale = plotHeight/(yTop-yLow) -# barWidth = xScale*step -# -# for i, count in enumerate(Count): -# if count: -# xc = (dataXY[i]-xLow)*xScale+xLeftOffset -# yc =-(count-yLow)*yScale+yTopOffset+plotHeight -# canvas.drawRect(xc+2,yc,xc+barWidth-2,yTopOffset+plotHeight,edgeColor=barColor,fillColor=barColor) -# -# #draw drawing region -# canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight) -# -# #draw scale -# scaleFont=pid.Font(ttf="cour",size=11,bold=1) -# x=xLow -# for i in range(stepX+1): -# xc=xLeftOffset+(x-xLow)*xScale -# canvas.drawLine(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, color=axesColor) -# strX = cformat(d=x, rank=0) -# canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+14,font=scaleFont) -# x+= (xTop - xLow)/stepX -# -# y=yLow -# for i in range(stepY+1): -# yc=yTopOffset+plotHeight-(y-yLow)*yScale -# canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor) -# strY = "%d" %y -# canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont) -# y+= (yTop - yLow)/stepY -# -# #draw label -# labelFont=pid.Font(ttf="tahoma",size=17,bold=0) -# if XLabel: -# canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0, -# yTopOffset+plotHeight+yBottomOffset-10,font=labelFont,color=labelColor) -# -# if YLabel: -# canvas.drawString(YLabel, 19, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0, -# font=labelFont,color=labelColor,angle=90) -# -# labelFont=pid.Font(ttf="verdana",size=16,bold=0) -# if title: -# canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0, -# 20,font=labelFont,color=labelColor) -# -#def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, sLabel = None, offset= (80, 20, 40, 100), barSpace = 2, zoom = 1): -# xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset -# plotWidth = canvas.size[0] - xLeftOffset - xRightOffset -# plotHeight = canvas.size[1] - yTopOffset - yBottomOffset -# if plotHeight<=0 or plotWidth<=0: -# return -# -# NNN = len(data) -# if NNN < 2 or NNN != len(label): -# return -# if variance and len(variance)!=NNN: -# variance = [] -# -# Y2 = data[:] -# if variance: -# for i in range(NNN): -# if variance[i]: -# Y2 += [data[i]-variance[i]] -# -# #Y axis -# YLow, YTop, stepY = detScale(min(Y2), max(Y2)) -# YScale = plotHeight/(YTop - YLow) -# -# if YLow < 0 and YTop > 0: -# drawZero = 1 -# else: -# drawZero = 0 -# -# #X axis -# X = range(NNN) -# Xll= 0 -# Xur= NNN-1 -# -# -# if drawZero: -# YZero = yTopOffset+plotHeight-YScale*(0-YLow) -# canvas.drawLine(xLeftOffset, YZero, xLeftOffset+plotWidth, YZero) -# else: -# YZero = yTopOffset+plotHeight -# #draw data -# spaceWidth = barSpace -# if spaceWidth < 1: -# spaceWidth = 1 -# barWidth = int((plotWidth - (NNN-1.0)*spaceWidth)/NNN) -# -# xc= xLeftOffset -# scaleFont=pid.Font(ttf="verdana",size=11,bold=0) -# for i in range(NNN): -# yc = yTopOffset+plotHeight-(data[i]-YLow)*YScale -# canvas.drawRect(xc,YZero,xc+barWidth-1, yc, edgeColor=barColor,fillColor=barColor) -# if variance and variance[i]: -# varlen = variance[i]*YScale -# if yc-varlen < yTopOffset: -# topYd = yTopOffset -# else: -# topYd = yc-varlen -# canvas.drawLine(xc+barWidth/2-2,yc-varlen,xc+barWidth/2+2,yc-varlen,color=pid.red) -# canvas.drawLine(xc+barWidth/2,yc+varlen,xc+barWidth/2,topYd,color=pid.red) -# canvas.drawLine(xc+barWidth/2-2,yc+varlen,xc+barWidth/2+2,yc+varlen,color=pid.red) -# strX = label[i] -# canvas.drawString(strX,xc+barWidth/2.0+2,yTopOffset+plotHeight+2+canvas.stringWidth(strX,font=scaleFont),font=scaleFont,angle=90) -# xc += barWidth + spaceWidth -# -# #draw drawing region -# canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight) -# -# #draw Y scale -# scaleFont=pid.Font(ttf="cour",size=16,bold=1) -# y=YLow -# for i in range(stepY+1): -# yc=yTopOffset+plotHeight-(y-YLow)*YScale -# canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor) -# strY = cformat(d=y, rank=0) -# canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont) -# y+= (YTop - YLow)/stepY -# -# #draw label -# labelFont=pid.Font(ttf="verdana",size=17,bold=0) -# if XLabel: -# canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,yTopOffset+plotHeight+65,font=labelFont,color=labelColor) -# -# if YLabel: -# canvas.drawString(YLabel,xLeftOffset-50, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,font=labelFont,color=labelColor,angle=90) -# -# labelFont=pid.Font(ttf="verdana",size=18,bold=0) -# if title: -# canvas.drawString(title,xLeftOffset,yTopOffset-15,font=labelFont,color=labelColor) -# -# return -# +def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1): + xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset + + plotWidth = canvas.size[0] - xLeftOffset - xRightOffset + plotHeight = canvas.size[1] - yTopOffset - yBottomOffset + if plotHeight<=0 or plotWidth<=0: + return + + if len(data) < 2: + return + + max_D = max(data) + min_D = min(data) + #add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong + if max_D == float('inf') or max_D>webqtlConfig.MAXLRS: + max_D=webqtlConfig.MAXLRS #maximum LRS value + + xLow, xTop, stepX = detScale(min_D, max_D) + + #reduce data + #ZS: Used to determine number of bins for permutation output + step = ceil((xTop-xLow)/50.0) + j = xLow + dataXY = [] + Count = [] + while j <= xTop: + dataXY.append(j) + Count.append(0) + j += step + + for i, item in enumerate(data): + if item == float('inf') or item>webqtlConfig.MAXLRS: + item = webqtlConfig.MAXLRS #maximum LRS value + j = int((item-xLow)/step) + Count[j] += 1 + + yLow, yTop, stepY=detScale(0,max(Count)) + + #draw data + xScale = plotWidth/(xTop-xLow) + yScale = plotHeight/(yTop-yLow) + barWidth = xScale*step + + for i, count in enumerate(Count): + if count: + xc = (dataXY[i]-xLow)*xScale+xLeftOffset + yc =-(count-yLow)*yScale+yTopOffset+plotHeight + canvas.drawRect(xc+2,yc,xc+barWidth-2,yTopOffset+plotHeight,edgeColor=barColor,fillColor=barColor) + + #draw drawing region + canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight) + + #draw scale + scaleFont=pid.Font(ttf="cour",size=11,bold=1) + x=xLow + for i in range(int(stepX)+1): + xc=xLeftOffset+(x-xLow)*xScale + canvas.drawLine(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, color=axesColor) + strX = cformat(d=x, rank=0) + canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+14,font=scaleFont) + x+= (xTop - xLow)/stepX + + y=yLow + for i in range(int(stepY)+1): + yc=yTopOffset+plotHeight-(y-yLow)*yScale + canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor) + strY = "%d" %y + canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont) + y+= (yTop - yLow)/stepY + + #draw label + labelFont=pid.Font(ttf="tahoma",size=17,bold=0) + if XLabel: + canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0, + yTopOffset+plotHeight+yBottomOffset-10,font=labelFont,color=labelColor) + + if YLabel: + canvas.drawString(YLabel, 19, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0, + font=labelFont,color=labelColor,angle=90) + + labelFont=pid.Font(ttf="verdana",size=16,bold=0) + if title: + canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0, + 20,font=labelFont,color=labelColor) + +def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, sLabel = None, offset= (80, 20, 40, 100), barSpace = 2, zoom = 1): + xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset + plotWidth = canvas.size[0] - xLeftOffset - xRightOffset + plotHeight = canvas.size[1] - yTopOffset - yBottomOffset + if plotHeight<=0 or plotWidth<=0: + return + + NNN = len(data) + if NNN < 2 or NNN != len(label): + return + if variance and len(variance)!=NNN: + variance = [] + + Y2 = data[:] + if variance: + for i in range(NNN): + if variance[i]: + Y2 += [data[i]-variance[i]] + + #Y axis + YLow, YTop, stepY = detScale(min(Y2), max(Y2)) + YScale = plotHeight/(YTop - YLow) + + if YLow < 0 and YTop > 0: + drawZero = 1 + else: + drawZero = 0 + + #X axis + X = range(NNN) + Xll= 0 + Xur= NNN-1 + + + if drawZero: + YZero = yTopOffset+plotHeight-YScale*(0-YLow) + canvas.drawLine(xLeftOffset, YZero, xLeftOffset+plotWidth, YZero) + else: + YZero = yTopOffset+plotHeight + #draw data + spaceWidth = barSpace + if spaceWidth < 1: + spaceWidth = 1 + barWidth = int((plotWidth - (NNN-1.0)*spaceWidth)/NNN) + + xc= xLeftOffset + scaleFont=pid.Font(ttf="verdana",size=11,bold=0) + for i in range(NNN): + yc = yTopOffset+plotHeight-(data[i]-YLow)*YScale + canvas.drawRect(xc,YZero,xc+barWidth-1, yc, edgeColor=barColor,fillColor=barColor) + if variance and variance[i]: + varlen = variance[i]*YScale + if yc-varlen < yTopOffset: + topYd = yTopOffset + else: + topYd = yc-varlen + canvas.drawLine(xc+barWidth/2-2,yc-varlen,xc+barWidth/2+2,yc-varlen,color=pid.red) + canvas.drawLine(xc+barWidth/2,yc+varlen,xc+barWidth/2,topYd,color=pid.red) + canvas.drawLine(xc+barWidth/2-2,yc+varlen,xc+barWidth/2+2,yc+varlen,color=pid.red) + strX = label[i] + canvas.drawString(strX,xc+barWidth/2.0+2,yTopOffset+plotHeight+2+canvas.stringWidth(strX,font=scaleFont),font=scaleFont,angle=90) + xc += barWidth + spaceWidth + + #draw drawing region + canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight) + + #draw Y scale + scaleFont=pid.Font(ttf="cour",size=16,bold=1) + y=YLow + for i in range(stepY+1): + yc=yTopOffset+plotHeight-(y-YLow)*YScale + canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor) + strY = cformat(d=y, rank=0) + canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont) + y+= (YTop - YLow)/stepY + + #draw label + labelFont=pid.Font(ttf="verdana",size=17,bold=0) + if XLabel: + canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,yTopOffset+plotHeight+65,font=labelFont,color=labelColor) + + if YLabel: + canvas.drawString(YLabel,xLeftOffset-50, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,font=labelFont,color=labelColor,angle=90) + + labelFont=pid.Font(ttf="verdana",size=18,bold=0) + if title: + canvas.drawString(title,xLeftOffset,yTopOffset-15,font=labelFont,color=labelColor) + + return + #def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, axesColor=pid.black, labelColor=pid.black, lineSize="thin", lineColor=pid.grey, idFont="arial", idColor=pid.blue, idSize="14", symbolColor=pid.black, symbolType="circle", filled="yes", symbolSize="tiny", XLabel=None, YLabel=None, title=None, fitcurve=None, connectdot=1, displayR=None, loadingPlot = 0, offset= (80, 20, 40, 60), zoom = 1, specialCases=[], showLabel = 1, bufferSpace = 15): # 'displayR : correlation scatter plot, loadings : loading plot' # diff --git a/wqflask/utility/external.py b/wqflask/utility/external.py new file mode 100644 index 00000000..50afea08 --- /dev/null +++ b/wqflask/utility/external.py @@ -0,0 +1,9 @@ +# Call external program + +import os +import sys +import subprocess + +def shell(command): + if subprocess.call(command, shell=True) != 0: + raise Exception("ERROR: failed on "+command) diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py new file mode 100644 index 00000000..67b84dc9 --- /dev/null +++ b/wqflask/utility/genofile_parser.py @@ -0,0 +1,100 @@ +# CTL analysis for GN2 +# Author / Maintainer: Danny Arends <Danny.Arends@gmail.com> + +from __future__ import print_function, division, absolute_import +import sys +import os +import glob +import traceback +import gzip + + +import simplejson as json + +from pprint import pformat as pf + +class Marker(object): + def __init__(self): + self.name = None + self.chr = None + self.cM = None + self.Mb = None + self.genotypes = [] + + +class ConvertGenoFile(object): + + def __init__(self, input_file): + self.mb_exists = False + self.cm_exists = False + self.markers = [] + + self.latest_row_pos = None + self.latest_col_pos = None + + self.latest_row_value = None + self.latest_col_value = None + self.input_fh = open(input_file) + print("!!!!!!!!!!!!!!!!PARSER!!!!!!!!!!!!!!!!!!") + self.haplotype_notation = { + '@mat': "1", + '@pat': "2", + '@het': "-999", + '@unk': "-999" + } + self.configurations = {} + + def process_rows(self): + for self.latest_row_pos, row in enumerate(self.input_fh): + self.latest_row_value = row + # Take care of headers + if not row.strip(): + continue + if row.startswith('#'): + continue + if row.startswith('Chr'): + if 'Mb' in row.split(): + self.mb_exists = True + if 'cM' in row.split(): + self.cm_exists = True + skip = 2 + self.cm_exists + self.mb_exists + self.individuals = row.split()[skip:] + continue + if row.startswith('@'): + key, _separater, value = row.partition(':') + key = key.strip() + value = value.strip() + if key in self.haplotype_notation: + self.configurations[value] = self.haplotype_notation[key] + continue + if not len(self.configurations): + raise EmptyConfigurations + yield row + + def process_csv(self): + for row_count, row in enumerate(self.process_rows()): + row_items = row.split("\t") + + this_marker = Marker() + this_marker.name = row_items[1] + this_marker.chr = row_items[0] + if self.cm_exists and self.mb_exists: + this_marker.cM = row_items[2] + this_marker.Mb = row_items[3] + genotypes = row_items[4:] + elif self.cm_exists: + this_marker.cM = row_items[2] + genotypes = row_items[3:] + elif self.mb_exists: + this_marker.Mb = row_items[2] + genotypes = row_items[3:] + else: + genotypes = row_items[2:] + for item_count, genotype in enumerate(genotypes): + if genotype.upper().strip() in self.configurations: + this_marker.genotypes.append(self.configurations[genotype.upper().strip()]) + else: + print("WARNING:", genotype.upper()) + this_marker.genotypes.append("NA") + self.markers.append(this_marker.__dict__) + diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index b8a41f60..dd8c4a1e 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -1,84 +1,137 @@ # Tools/paths finder resolves external paths from settings and/or environment # variables -# -# Currently supported: -# -# PYLMM_PATH finds the root of the git repository of the pylmm_gn2 tool import os import sys from wqflask import app -def get_setting(id,default,guess,get_valid_path): - """ - Resolve a setting from the environment or the global settings in app.config +def get_setting(command_id,guess=None): + """Resolve a setting from the environment or the global settings in + app.config, with get_valid_path is a function checking whether the + path points to an expected directory and returns the full path to + the binary command + + guess = os.environ.get('HOME')+'/pylmm' + get_setting('PYLMM_PATH',guess) + + first tries the environment variable in +id+, next gets the Flask + app setting for the same +id+ and finally does an educated + +guess+. + + In all, the environment overrides the others, next is the flask + setting, then the guess. A valid path to the binary command is + returned. If none is resolved an exception is thrown. + + Note that we do not use the system path. This is on purpose + because it will mess up controlled (reproducible) deployment. The + proper way is to either use the GNU Guix defaults as listed in + etc/default_settings.py or override them yourself by creating a + different settings.py file (or setting the environment). + """ + def value(command): + if command: + sys.stderr.write("Found path "+command+"\n") + return command + else: + return None + # ---- Check whether environment exists - path = get_valid_path(os.environ.get(id)) - # ---- Check whether setting exists - setting = app.config.get(id) - if not path: - path = get_valid_path(setting) - # ---- Check whether default exists - if not path: - path = get_valid_path(default) - # ---- Guess directory - if not path: - if not setting: - setting = guess - path = get_valid_path(guess) - if not path: - raise Exception(id+' '+setting+' path unknown or faulty (update settings.py?). '+id+' should point to the root of the git repository') - - return path - -def pylmm_command(default=None): + sys.stderr.write("Looking for "+command_id+"\n") + command = value(os.environ.get(command_id)) + if not command: + # ---- Check whether setting exists in app + command = value(app.config.get(command_id)) + if not command: + command = value(guess) + if not command: + raise Exception(command_id+' path unknown or faulty (update settings.py?). '+command_id+' should point to the path') + return command + +def valid_bin(bin): + if os.path.islink(bin) or valid_file(bin): + return bin + return None + +def valid_file(fn): + if os.path.isfile(fn): + return fn + return None + +def valid_path(dir): + if os.path.isdir(dir): + return dir + return None + +def pylmm_command(guess=None): + return valid_bin(get_setting("PYLMM_COMMAND",guess)) + +def gemma_command(guess=None): + return valid_bin(get_setting("GEMMA_COMMAND",guess)) + +def plink_command(guess=None): + return valid_bin(get_setting("PLINK_COMMAND",guess)) + +def flat_files(subdir=None): + base = get_setting("GENENETWORK_FILES") + if subdir: + return assert_dir(base+"/"+subdir) + return assert_dir(base) + +def assert_dir(dir): + if not valid_path(dir): + raise Exception("ERROR: can not find directory "+dir) + return dir + +def mk_dir(dir): + if not valid_path(dir): + os.makedirs(dir) + return assert_dir(dir) + +def locate(name, subdir=None): """ - Return the path to the repository and the python command to call + Locate a static flat file in the GENENETWORK_FILES environment. + + This function throws an error when the file is not found. """ - def get_valid_path(path): - """Test for a valid repository""" - if path: - sys.stderr.write("Trying PYLMM_PATH in "+path+"\n") - if path and os.path.isfile(path+'/pylmm_gn2/lmm.py'): - return path + base = get_setting("GENENETWORK_FILES") + if subdir: + base = base+"/"+subdir + if valid_path(base): + lookfor = base + "/" + name + if valid_file(lookfor): + print("Found: file "+lookfor+"\n") + return lookfor else: - None + raise Exception("Can not locate "+lookfor) + if subdir: sys.stderr.write(subdir) + raise Exception("Can not locate "+name+" in "+base) - guess = os.environ.get('HOME')+'/pylmm_gn2' - path = get_setting('PYLMM_PATH',default,guess,get_valid_path) - pylmm_command = 'python '+path+'/pylmm_gn2/lmm.py' - return path,pylmm_command - -def plink_command(default=None): +def locate_ignore_error(name, subdir=None): """ - Return the path to the repository and the python command to call + Locate a static flat file in the GENENETWORK_FILES environment. + + This function does not throw an error when the file is not found + but returns None. """ - def get_valid_path(path): - """Test for a valid repository""" - if path: - sys.stderr.write("Trying PLINK_PATH in "+path+"\n") - if path and os.path.isfile(path+'/plink'): - return path - else: - None - - guess = os.environ.get('HOME')+'/plink_gemma' - path = get_setting('PLINK_PATH',default,guess,get_valid_path) - plink_command = path+'/plink' - return path,plink_command - -def gemma_command(default=None): - def get_valid_path(path): - """Test for a valid repository""" - if path: - sys.stderr.write("Trying PLINK_PATH in "+path+"\n") - if path and os.path.isfile(path+'/plink'): - return path - else: - None + base = get_setting("GENENETWORK_FILES") + if subdir: + base = base+"/"+subdir + if valid_path(base): + lookfor = base + "/" + name + if valid_file(lookfor): + print("Found: file "+name+"\n") + return lookfor + sys.stderr.write("WARNING: file "+name+" not found\n") + return None + +def tempdir(): + return valid_path(get_setting("TEMPDIR","/tmp")) - guess = os.environ.get('HOME')+'/plink' - path = get_setting('PLINK_PATH',default,guess,get_valid_path) - gemma_command = path+'/gemma' - return path, gemma_command \ No newline at end of file + +# Cached values +PYLMM_COMMAND = pylmm_command() +GEMMA_COMMAND = gemma_command() +PLINK_COMMAND = plink_command() +FLAT_FILES = flat_files() +TEMPDIR = tempdir() diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py index f842dde0..1108614b 100755 --- a/wqflask/utility/webqtlUtil.py +++ b/wqflask/utility/webqtlUtil.py @@ -509,7 +509,7 @@ def calCorrelationRank(xVals,yVals,N): j = 0 for i in range(len(xVals)): - if xVals[i]!= None and yVals[i]!= None: + if (xVals[i]!= None and yVals[i]!= None) and (xVals[i] != "None" and yVals[i] != "None"): XX.append((j,xVals[i])) YY.append((j,yVals[i])) j = j+1 |