Fatomum.py
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#!/usr/bin/env python
#############################################################################################################################
#fatomum.py [options] <fasta file containing alignment> #
#Example: python fatomum.py -p ../myAlignment.fsa #
#Version: 1.0 Last Modified: 1/15/2010 Author: Zachary S. L. Foster #
#---------------------------------------------------------------------------------------------------------------------------#
#>Argument: Path to a FASTA file containing a reference and its aligned contigs #
#---------------------------------------------------------------------------------------------------------------------------#
#>Creates a MUMmer-style output from a FASTA file of aligned sequences #
#>The first line is always considered the reference and is not included in the output #
#>The start index in terms of the reference, and in terms of the contig, as well as the length are recorded for each #
# matching section of the contig #
#---------------------------------------------------------------------------------------------------------------------------#
#Modifiers: #
# -d : save debug log; specify where to save the debug log (default = current working directory) #
# -p : print output #
# -m : set minimum match length; anything less will not be included in the output; default = 10 #
#############################################################################################################################
###Imports / Variable Initilization##########################################################################################
import os, string, sys, time
defArgList = ['fatomum.py','-p','-m','300','C:/Python26/balf.yasrahigh.koraref.CCassembly.fasta'] #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
saveDebug = 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 log
printOut = False #is True when no the -p modifier is supplied; #The results will be printed to the standard output (usually the screen)
helpOnly = False #is 'True' when no arguments are given; only help menu is printed
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 = 'dpm' #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
faData = [] #will contain a list of each contig and its name
outData = [] #eventually holds the data that will be saved in the output file
debugLog = ['***********DEBUG LOG***********\n'] #where all errors/anomalies are recorded; saved if the -d modifier is supplied
minMatchLen = 20 #minimum match length; anything less will not be included in the output
#############################################################################################################################
#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 prematurely, printing debug log...\n'
for line in debugLog:
print line
sys.exit()
#############################################################################################################################
def printHelp():
print '/---------------------------------------------------------------------------------------\\'
print '| fatomum.py [options] <fasta file containing alignment> |'
print '|---------------------------------------------------------------------------------------|'
print '| Example: python fatomum.py -p ../myAlignment.fsa |'
print '|---------------------------------------------------------------------------------------|'
print '| Version: 1.0 Last Modified: 1/15/2010 Author: Zachary S. L. Foster |'
print '| >Creates a MUMmer-style output from a FASTA file of aligned sequences |'
print '| >The first line is always considered the reference and is not included in the output |'
print '|---------------------------------------------------------------------------------------|'
print '| Modifiers: |'
print '| -d : Save debug log |'
print '| -p : Print output to standard out (usually the shell being called from) |'
print '| -m : set minimum match length; anything less will not be considered a match; |'
print '| default = 10 |'
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
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: default 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: #checks if the modifiers are recognized
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 letter == 'd': #if -d is supplied...
saveDebug = True #The debug log will be saved to the current working directory
if letter == 'p': #if -p is supplied...
printOut = True #The results will be printed to the standard output (usually the screen)
if letter == 'm': #if -n is supplied...
if len(modArgs) > 0: #if there is at least one non-processed modifier argument
minMatchLen = int(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 and parsing################################################################################
faHandle = open(faPath, 'r') #opens the input data file
faRaw = faHandle.readlines() #all information is transferred to faRaw
faHandle.close() #file object is closed
faRaw.append('> ') #allows the loop to process the last contig
cntgSeq = ''
for line in faRaw:
if line[0] == '>': #if the line is the name of a contig...
if len(cntgSeq) > 0: #if there is sequence saved from the previous contig
faData.append([cntgName,cntgSeq]) #add the previous contig to the list
cntgSeq = '' #clear the old sequence
cntgName = line[:-1] #new contig name is saved, [:-1] removes '\n'
else: #if the line is a sequence...
if line[0] == ' ': # if there is a space at the start of the line...
line = line[1:] #remove the space
cntgSeq += line[:-1] #add the sequence to any previous sequence encountered
reference = faData[0] #the first sequence is assumed to be the reference
#########################################################################################################################
###MUMmer output emulation###############################################################################################
outData = []
for contig in faData[1:]: #for every sequence except the reference...
cntgMatches = [] #a list of match data for each contig
name = contig[0] #name of the contig
index = 0 #reference base index
inMatch = False #if True, then the current base index contains a match
refStart = 0 #the reference index of the first base of a match
cntgStart = 0 #the contig index of the first base of a matches
length = 0 #the length of the match
firstSeqIndex = 0 #the first index of the contig that is not a '-'
while contig[1][firstSeqIndex] == '-':
firstSeqIndex += 1
for bp in contig[1]: #for every base pair...
if inMatch == True:
if ( bp == '-' or bp != reference[1][index] ): #if the current base is '-' or does not match the reference, while in a match,
inMatch = False #therefore, not in a match
length = index - refStart #calculate the length of the match, index is the base after the last base of the match
if length >= minMatchLen: #if the match is long enough to be included in the output...
cntgMatches.append([refStart,cntgStart,length]) #include it
elif bp != '-' and index < len(reference[1]) and bp == reference[1][index]: #if not in a match, but the currrent base is not '-' and matches the reference..
inMatch = True #in a new match
refStart = index #record start
cntgStart = refStart - firstSeqIndex #start in terms of the contig
index +=1
outData.append(name) #adds the name to the output, regardless of whether the contig has any matchs or not
for match in cntgMatches: #if every match on this contig...
outData.append(' ' + str(match[0]) + '\t' + str(match[1]) + '\t' + str(match[2])) #record a string version for the output
#########################################################################################################################
###Out file writing and saving procedures###############################################################################
fileSavePath = savePath + os.path.basename(faPath) + '.fsa' #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 outSeqs to the output file...
outHandle.write(line)
if printOut: #if the -p modifier is supplied...
for line in outData:
print line
outHandle.close() #closes file object
#########################################################################################################################
###Debug Saving procedures###############################################################################################
if saveDebug: #if the -d modifier is supplied...
debugHandle = open(savePath + os.path.basename(qualPath) + '_debug.txt', 'w')
for line in debugLog:
debugHandle.write(line)
debugHandle.close()
#########################################################################################################################
