Basediff.py
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Copy and past the following into a text editor and save it as basediff.py to use the script.
#!/usr/bin/env python
#############################################################################################################################
#basediff.py [options] <path to aligned fasta file> #
#Example: python basediff.py -i -# 1,2-5,7-9 ../myFile.fsa #
#Version: 1.2 Last Modified: 12/22/2009 #
#---------------------------------------------------------------------------------------------------------------------------#
#>Argument 1: path to fasta file containing aligned sequences #
#---------------------------------------------------------------------------------------------------------------------------#
#>Finds base differences between aligned sequences in a single file #
#>Output a tab-delimitated list of differing sets of bases #
#---------------------------------------------------------------------------------------------------------------------------#
#Modifiers: #
# -d : include differences caused by - or ~ #
# -i : include differences caused by IUPAC nucleic acid codes #
# -n : include differences caused by N's #
# -p : print output #
# -s : include differences caused by absence of sequence (aka unequal sequence length) #
# -# arg : specify which sequences in a file to compare; Example: -# 1,2,5-9,11 #
#############################################################################################################################
###Imports / Variable Initilization##########################################################################################
import os, string, sys, time
defArgList = ['basediff.py','-s','C:/Python26/basediffdef.fa'] #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
warning = False #is set to 'True' if the program encounters any minor errors during the analysis
printOut = False #is set to 'True' if the '-p' modifier is used
helpOnly = False #is set to 'True' if no arguments are supplied; causes the help text to be printed
compChars = 'AGTCU' #All the nucleic acid codes recognized by the script; expanded by the -i, -n, and -d modifiers
lineNumIn = 'ALL' #contains the input for the '-#' modifier, specifies which lines in the input file are used in the analysis
savePath = './' #the directory in which the output will be saved
defSavePath = 'C:/Python26/' #save path used during script testing with the python GUI IDLE
modifiers = [] #eventually contains a list of all modifiers and their arguments supplied by the user
allMods = 'dinps#' #all the modifiers recognized by the script
activeMods = '' #a string containing all modifiers specified by the user
modArgs = [] #arguments supplied for the modifiers; assumed in the same order as the modifiers
#############################################################################################################################
def printHelp():
print '/---------------------------------------------------------------------------------------\'
print '| basediff.py [options] <path to aligned fasta file> |'
print '|---------------------------------------------------------------------------------------|'
print '| Example: python basediff.py -i -# 1,2-5,7-9 ../myFile.fsa |'
print '|---------------------------------------------------------------------------------------|'
print '| Version: 1.2 Last Edited: 12/21/2009 |'
print '|\t>Finds base differences between aligned sequences in a single file |'
print '|\t>Output a tab-delimitated list of differing sets of bases |'
print '|---------------------------------------------------------------------------------------|'
print '| Modifiers: |'
print '|\t-d\t: include differences caused by - or ~ |'
print '|\t-i\t: include differences caused by IUPAC nucleic acid codes |'
print '|\t-n\t: include difference caused by Ns |'
print '|\t-p\t: print output |'
print '|\t-s\t: include differences caused by absence of sequence (aka unequal sequence length)|'
print '|\t-#\t: specify which sequences in a file to compare. ex: -# 1-3,5,9 |'
print '\---------------------------------------------------------------------------------------/'
###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
print 'Error: Invalid file path to input fasta file'
sys.exit() #end the program
elif argNum == 1: #If no arguments are supplied...
helpOnly = True
printHelp() #prints help menu
else:
print 'Error: Too few arguments supplied\n'
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
print '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
print 'argument not recognized' #if the input modifier is not found
else: #if it is a recognized modifier...
if letter == 'd': #if -d is supplied...
compChars += '-~' #-'s and ~'s are recognized by the script
if letter == 'i': #if -i is supplied...
compChars += 'RYMKWSBDHV' #IUPAC nucleic acid codes are recognized by script
if letter == 'n': #if -n is supplied...
compChars += 'N' #N's are recognized by the script
if letter == 'p': #if -p is supplied...
printOut = True #The results will be printed to the standard output (usually the screen)
if letter == 's': #if -s is supplied...
compChars += ' ' #absence of sequence, caused by sequences of diffrent length, is considered a difference
if letter == '#': #if -# is supplied...
if len(modArgs) > 0: #if there is at least one non-processed modifier argument
lineNumIn = modArgs[0] #The string specifying the desired lines to process from the input file
del modArgs[0] #the original argument is deleted from the list
else: #if the list of modifier arguments is empty...
print 'Error: Modifier argument not supplied\n'
sys.exit() #exit the script
#########################################################################################################################
###Input data file procedures############################################################################################
#>extracts the input data from the files at the supplied path #
#>Parses the data into a list in the following format [[name of contig, sequence],[..]..] #
#>interprates the -# modifier's argument and applies its effects to the parsed list #
faHandle = open(faPath, 'r') #creates a file object
faRaw = faHandle.readlines() #all of the content of the input file in its raw form
faData = [] #will hold all data from faRaw in the following format [[name of contig, sequence],[..]..]
faFinal = [] #will hold the the lines from faData that lineNumIn specifies (if -# modifier is supplied)
faHandle.close() #closes the file object
faRaw.append('>') #makes it so the last sequence can be processed in the following loop
name = faRaw[0][:-1] # initialized the variable for the loop, so that the first sequence can be included
seq = ''
for line in faRaw[1:]: #loops through the lines of the input file
if line[0] == '>': #if the first character of the line is a '>'
faData.append([name,seq])
name = line[:-1]
seq = ''
else:
seq += line[:-1]
if lineNumIn == 'ALL': #if the -# modifier is not supplied
faFinal = faData #all lines are included in the analysis
else: # if the -# modifier is supplied
indexList = []
for num in string.split(lineNumIn,','): #loops through each entry separated by commas of the -# argument (e.g. 1,2,3-5,7)
if string.find(num,'-') != -1: #if the entry is a range of values
startNum = int(string.split(num,'-')[0]) #starting value of the range
endNum = int(string.split(num,'-')[-1]) #ending value of the range
while startNum <= endNum: #repeats for each value from start to end (inclusive)
indexList.append(startNum - 1) #include the information at the current value in faFinal
startNum += 1
else: #if the entry is just a single number
indexList.append(int(num) - 1) #include the information of that value in faFinal
for index in indexList:
if index < len(faData):
faFinal.append(faData[index]) #include the information of that value in faFinal
#########################################################################################################################
###Base-by-base comparision##############################################################################################
#>Finds the indices at which there are disagreements between the sequences and saved them in a list #
maxLen = 0 #will hold the length of the longest contig
outIndexs = [] #a list of of the indices at which differences occur
for cntg in faFinal: #loops through the contigs and finds the maximum length...
if len(cntg[1]) > maxLen:
maxLen = len(cntg[1])
for index in range(0,maxLen): #loops through the sequence indices
first = faFinal[0][1][index] #save the character at "index" in the first contig for comparison
for cntg in faFinal: #loops through the contigs (still at a specific index)
if index >= len(cntg[1]): #if the length of the contig sequence is less than the current index being tested...
cntg[1] += ' ' #the space character is used to indicate a lack of sequence
if string.find(compChars,cntg[1][index].upper())!= -1: #if the character at "index" in "cntg" is included in the recognized characters
if first != cntg[1][index]: #if the character in the first contig is different from that at the same index in a different contig...
outIndexs.append(index) #add the index of the difference to the outIndexs list
break
#########################################################################################################################
###Output data generation################################################################################################
#>generates the text used in the output from the data of the previous section, "Base-by-base comparison" #
#>the schema is as follows: Base#\tContigName1\tContigName2\tContigName3... #
outData = [] #a list of strings corresponding to each line in the output file
schema = 'Base#' #Will hold the first line of the output file
for cntg in faFinal: #for every contig...
schema += '\t' + cntg[0][1:] #add the name of the contig to the schema
outData.append(schema) #write the schema to outData
for index in outIndexs: #loops through the indicies of the bases determined to be diffrent in the above section
baseOut = str(index + 1) #a string version of the index starting from 1 intead of 0
for cntg in faFinal: #loops through all of the contigs
#print index
#print cntg
if index < len(cntg[1]):
baseOut += '\t' + str(cntg[1][index]) #adds the base value to the line, separated by tabs
outData.append(baseOut)
#########################################################################################################################
###Out file writing and saveing procedures###############################################################################
fileSavePath = savePath + 'BaseDiff.' + os.path.basename(faPath) + '.txt' #the path to where the output is saved
outHandle = open(fileSavePath, '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 + '\n')
outHandle.close()
if printOut: #if the -p modifier is supplied
for line in outData: #prints every line to the standard output
print line
#########################################################################################################################
