BPstats.py
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Copy and past the following into a text editor and save it as BPstats.py to use the script.
#!/usr/bin/env python
#############################################################################################################################
#BPstats.py [options] <basepile output> #
#Example: python BPstats.py -p -h myBasePile.txt #
#Version: 1.2 Last Modified: 12/21/2009 #
#---------------------------------------------------------------------------------------------------------------------------#
#>Ouptuts a txt file containing statistics in the following format: #
# GSS basepile #\tGSS ref match length\ttarget match sum\tcoverage proportion\taverage density of target\tmedian densitiy #
#>Assumes each contig is 1000 bases long #
#---------------------------------------------------------------------------------------------------------------------------#
#Modifiers: #
# -d : Save debug log #
# -h : Do not print header on first line #
# -p : Print output to standard out (usually the shell being called from) #
# -r : Make output more readable by adding extra tabs to the statistic columbs (aligns columbs to header) #
#############################################################################################################################
###Imports / Variable Initilization##########################################################################################
import os, string, sys
defArgList = ['BPstats.py','-H','C:/Python26/testData.txt'] #argument list used during script testing the with Python GUI IDLE
argList = sys.argv #argument list supplied by user
argNum = len(argList) #the number of arguments supplied
minArgNum = 1 #the smallest amount of arguments with which it is possible to run the script
addHead = True #is True if the headers are to be printed on the first line
saveDubug = False #is True if the debug is to be saved
warning = False #is set to 'True' if the program encounters any minor errors during the analysis; recorded in debug law
readable = False #is 'True' if the -r modifier is supplied; makes the output easier to read
debugLog = ['*********DEBUG LOG*********\n'] #where all errors/anamolies are recorded; saved if the -d modifier is supplied
savePath = './' #the directory in which the output will be saved
defSavePath = 'C:/Python26/' #save path used during script testing with the python GUI IDLE
header = 'Contig #\tRef length\tMatch sum\tCoverage %\tAve density \tMed density\n' #the header which is printed on the first line of the output
inData = [] #a list of lists contiaing the data from the input file [[ref,density,actual],...]
parsedData = [] #a list containing data for each 1000 bp chunk [[GSS ref match length...see above]...]
outData = [] #a list of strings corresponding to each line in the output file
modifiers = [] #eventually contains a list of all modifiers and their arguments supplied by the user
allMods = 'hpr' #all the modifiers reconized by the script
activeMods = '' #a string contiaing all mods specified by the user
modArgs = [] #arguments supplied for the modifiers; assumed in the same order as the modifiers
#############################################################################################################################
def printHelp():
print '/---------------------------------------------------------------------------------------\'
print '| BPstats.py [options] <basepile output> |'
print '|---------------------------------------------------------------------------------------|'
print '| Example: python BPstats.py -p -h myBasePile.txt |'
print '|---------------------------------------------------------------------------------------|'
print '| Version: 1.2 Last Edited: 12/22/2009 |'
print '|\t>Ouptuts a txt file containing statistics in the following format: |'
print '|\t\tGSS basepile #, GSS ref match length, target match sum, coverage proportion, |'
print '|\t\taverage density of target, median densitiy |'
print '|\t>Assumes each contig is 1000 bases long |'
print '|---------------------------------------------------------------------------------------|'
print '| Modifiers: |'
print '|\t-d\t: Save debug log |'
print '|\t-h\t: Do not print header on first line |'
print '|\t-p\t: Print output to standard out (usually the shell being called from) |'
print '|\t-r\t: Make output more readable by adding extra tabs to the output columbs |'
print '\---------------------------------------------------------------------------------------/'
#Error handling function#####################################################################################################
#>Is called when the script encounters a fatal error #
#>Prints the debug log to standard out (usually the screen) #
def errorExit():
print 'The program was forced to exit prematurly, printing debug log...\n'
for line in debugLog:
print line
sys.exit()
#############################################################################################################################
###Argument Interprtation####################################################################################################
#>Parses the arguments supplied by the user, or the default values if the script is being run on IDLE #
#>If no arguments are given, the help menu is printed #
#>Modifiers and their arguments are isolated from the raw input for later processing (in Modifier Interpretation) #
if __name__ == '__main__': #If the program is being called independent of the Python GUI, IDLE...
if argNum > minArgNum: #If at least the minimum number of arguments necessary is supplied...
if os.path.exists(argList[-1]) == 0: #if the path dose not exist
debugLog.append('Error: Invalid file path to input data')
errorExit() #end the program
elif argNum == 1: #If no arguments are supplied...
helpOnly = True
printHelp() #prints help menu
else:
debugLog.append('Error: Too few arguments supplied\n')
errorExit()
else: #If the script is being imported on to IDLE
argList = defArgList #use default arguments
argNum = len(defArgList)
if argNum == 1: #If no arguments are supplied...
helpOnly = True
printHelp() #prints help menu
savePath = defSavePath #sets the save path to the default, specified in the variable initialization section
debugLog.append('Alert: defualt debugging input arguments are being used\n')
if helpOnly == False: #if arguments were supplied...
faPath = argList[-1] #the path to the fasta file containing the input data
if argNum > minArgNum + 1: #if modifiers are present (i.e. more the minimum number of arguments)
modifiers = argList[1:-minArgNum] #everything before the required arguments are modifiers and their arguments
#############################################################################################################################
if helpOnly == False:
###Modifier Interpretation###############################################################################################
#>Parses any modifiers and modifier arguments determined by the previous section of code, "Argument Interpretation" #
#>Given arguments are compared against a list of known arguments #
#>Matches found change the appropriate variable for the desired effect of the modifier the script #
if len(modifiers) > 0: #if modifiers are supplied
for mod in modifiers: #loops through the list of modifiers and modifier arguments
if mod[0] == '-' and len(mod) == 2: #list entry considered modifier if it starts with - and is only two characters
activeMods += mod[1:] #sorts the modifiers into activeMods...
else:
modArgs.append(mod) #assumes everything else to be a modifier argument
for letter in activeMods: #loops through supplied modifiers
if string.find(allMods,letter) == -1: #checks if the modifier is recognized by this script
debugLog.append('Warning: Unexpected modifier: ' + letter + '\n')
warning = True #if the input modifier is not found
else: #if it is a recognized modifier...
if letter == 'd': #if -d is supplied...
saveDebug = True #The debug log will be saved to the current working directory
if letter == 'h': #if -h is supplied...
printHead = False #header will not be included in the output
if letter == 'p': #if -p is supplied...
printOut = True #The results will be printed to the standard output (usually the screen)
if letter == 'r': #if -r is supplied...
readable = True #columbs are spaced in a more readable way
#########################################################################################################################
###Input data parseing and file procedures###############################################################################
inHandle = open(inPath, 'r') #creates a file object
inHandle.readline() #moves position past the header on the first line
for line in inHandle: #loops through the lines of the input file
lineParts = string.split(line) #produces a list of all the contents of each line (separated by spaces/abs)
reference = lineParts[1]
actual = lineParts[6]
density = 0
for index in range(2,6): #adds the middle 4 values together to obtain density
density += int(lineParts[index])
inData.append([reference,density,actual]) #adds parsed line to the list that will be analysed
inHandle.close() #closes the file object
#outputs [[ref,density,actual],...]
#########################################################################################################################
###Statistical analysis##################################################################################################
contigNum = len(inData)/1000 #The number of contigs the base pile output represents
for count in range(0,contigNum): #do once for every contig
contig = inData[count * 1000:(count + 1) * 1000] #isolates the parsed input data specific to that contig
refMatchLen = 0 #records the index of the last known base on the reference
tarMatchSum = 0 #counts how many known (not N) bases match the target
medDensity = 0 #median density value for the contig
index = 0
denList = [] #a list of all the densities for this contig; used to get median and average density
for bp in contig: #for every base in the contig...
denList.append(bp[1]) #record its density value
if bp[0] != 'N': #if the actual value is known...
refMatchLen = index #the length of the viable portion of the reference that is known
if bp[2] != 'N' and bp[0] == bp[2]: #if the actual value is known and equals the reference...
tarMatchSum += 1 #increment the amount of matching bases
index += 1 #incremented to match the index of the current base pair
denList.sort() #allows for the median calculation
coveragePro = float(tarMatchSum) / float(refMatchLen) #percentage of the actual that matchs to the reference
aveDensity = float(sum(denList)) / float(refMatchLen) #average density values within the known portion of the reference
medDensity = float(denList[499] + denList[500]) / 2 #median density of the entire range of density values
contigStats = []
contigStats.append(count + 1) #GSS basepile #
contigStats.append(refMatchLen)
contigStats.append(tarMatchSum)
contigStats.append(coveragePro)
contigStats.append(aveDensity)
contigStats.append(medDensity)
parsedData.append(contigStats)
#outputs: [[GSS basepile #,GSS ref match length,target match sum,coverage proportion,average density of target,median densitiy]...]
#########################################################################################################################
def round(dec): #basic rounding function
outDec = dec
decPos = string.find(dec,'.')
if decPos != -1 and len(dec) > (decPos + 3):
outDec = outDec[:decPos + 3]
return outDec
###Data-to-Text Formating################################################################################################
for contig in parsedData: #for every contig
contigText = ''
for stat in contig: #for every statistic in each contig
statText = round(str(stat)) #round to three significant figures
contigText += statText + '\t' #add the statistic to the output for this contig
if readable: #if the -r modifier is supplied
contigText += '\t' #add an extra tab to make the columbs align to the header
contigText = contigText[:-1] #removes last \t
if readable: #if the -r modifier is supplied
contigText = contigText[:-1] #remove the extra tab
contigText += '\n' #add an endline after the statistics of each contig
outData.append(contigText) #add the contig to the output data
#########################################################################################################################
###Out file writing and saveing procedures###############################################################################
savePath += os.path.basename(inPath)[:-4] + '_stats.txt' #the path to where the output is saved
outHandle = open(savePath, 'w') #opens the file object for saving the output
for line in outData: #prints every line of outData to the output file...
outHandle.write(line)
outHandle.close()
if printOut: #if the -p modifier is supplied
for line in outData: #prints every line to the standard output...
print line[:-1]
#########################################################################################################################
