Basediff.py

Copy and past the following into a text editor and save it as basediff.py to use the script.
 * 1) !/usr/bin/env python


 * 1) basediff.py [options]                                                                         #
 * 2) Example: python basediff.py -i -# 1,2-5,7-9 ../myFile.fsa                                                                 #
 * 3) Version: 1.2  Last Modified: 12/22/2009                                                                                   #
 * 4) >Argument 1: path to fasta file containing aligned sequences                                                              #
 * 5) >Finds base differences between aligned sequences in a single file                                                        #
 * 6) >Output a tab-delimitated list of differing sets of bases                                                                 #
 * 7) Modifiers:                                                                                                                #
 * 8)   -d      : include differences caused by - or ~                                                                          #
 * 9)   -i      : include differences caused by IUPAC nucleic acid codes                                                        #
 * 10)   -n      : include differences caused by N's                                                                             #
 * 11)   -p      : print output                                                                                                  #
 * 12)   -s      : include differences caused by absence of sequence (aka unequal sequence length)                               #
 * 13)   -# arg  : specify which sequences in a file to compare; Example: -# 1,2,5-9,11                                          #
 * 1)   -n      : include differences caused by N's                                                                             #
 * 2)   -p      : print output                                                                                                  #
 * 3)   -s      : include differences caused by absence of sequence (aka unequal sequence length)                               #
 * 4)   -# arg  : specify which sequences in a file to compare; Example: -# 1,2,5-9,11                                          #

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
 * 1) Imports / Variable Initilization##########################################################################################

def printHelp: print '/---\' print '| basediff.py [options]                                    |' 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 '\---/'

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
 * 1) Argument Interprtation####################################################################################################
 * 2) >Parses the arguments supplied by the user, or the default values if the script is being run on IDLE                      #
 * 3) >If no arguments are given, the help menu is printed                                                                      #
 * 4) >Modifiers and their arguments are isolated from the raw input for later processing (in Modifier Interpretation)          #

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 #########################################################################################################################