Baseanno.py
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Copy and past the following into a text editor and save it as baseanno.py to use the script.
#!/usr/bin/env python
#############################################################################################################################
#baseanno.py [options] <text file with annotations and start/end indices> #
#Example: python baseanno.py -p myAnnotations.txt #
#Version: 1.0 Last Modified: 12/22/2009 Author: Zachary S. L. Foster #
#---------------------------------------------------------------------------------------------------------------------------#
#Argument: a whitespace-delimitated text (.txt) file which contains a list of annotations in the following format: #
# Annotation Start index End index ... #
# *The name of the annotation have no spaces; if it does, use the -t modifier #
#---------------------------------------------------------------------------------------------------------------------------#
#>Outputs a tab-delimitated list of base indices and their respective annotations #
#>If a single base has more than one annotation, then the additional annotations are added after the first on the same line #
#---------------------------------------------------------------------------------------------------------------------------#
#Modifiers: #
# -d : Save debug log to current working directory #
# -p : Print output to standard out (usually the shell/screen being called from) #
# -t : Use if the name of your annotations have spaces AND the input data is tab-delimitated #
#############################################################################################################################
###Imports / Variable Initilization##########################################################################################
import os, string, sys
defArgList = ['baseanno.py','-p','-t','C:/Python26/baseannoTestData.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
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 log
tabDelim = False #is 'True' if the -t modifier is supplied; enforces tab-delimitation in input file
helpOnly = False #is 'True' when no arguments are given; only help menu is printed
debugLog = ['*********DEBUG LOG*********\n'] #where all errors/anomalies 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
inData = [] #a list of lists containing 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 = 'dpt' #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 '| baseanno.py [options] <text file with annotations and start/end indices> |'
print '|---------------------------------------------------------------------------------------|'
print '| Example: python baseanno.py -p myAnnotations.txt |'
print '|---------------------------------------------------------------------------------------|'
print '| Version: 1.0 Last Edited: 12/22/2009 |'
print '| >Outputs a tab-delimitated list of base indices and their respective annotations |'
print '| >If a single base has more than one annotation, then the additional annotations are |'
print '| added after the first on the same line |'
print '|---------------------------------------------------------------------------------------|'
print '| Modifiers: |'
print '| -d : Save debug log |'
print '| -p : Print output to standard out (usually the shell being called from) |'
print '| -t : Use if your annotations have spaces AND the input data is tab-delimitated |'
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 prematurely, 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: default debugging input arguments are being used\n')
if helpOnly == False: #if arguments were supplied...
inPath = 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 == 'p': #if -p is supplied...
printOut = True #The results will be printed to the standard output (usually the screen)
if letter == 't': #if -t is supplied...
tabDelim = True #tab-delimitation is enforced for input file
#########################################################################################################################
###Input data parseing and file procedures###############################################################################
inHandle = open(inPath, 'r') #creates a file object
for line in inHandle: #loops through the lines of the input file
if tabDelim:
lineParts = string.split(line,'\t') #produces a list of all the contents of each line (delimitated by tabs only)
else:
lineParts = string.split(line) #produces a list of all the contents of each line (delimitated by spaces/tabs)
if len(lineParts) >= 3:
annotation = lineParts[0]
start = int(lineParts[1])
end = int(lineParts[2])
inData.append([annotation,start,end]) #adds parsed line to the list that will be analyzed
inHandle.close() #closes the file object
#########################################################################################################################
###Consensous creation###################################################################################################
outData = []
lastBaseIndex = 0
for anno in inData:
if anno[2] > lastBaseIndex:
lastBaseIndex = anno[2]
for index in range(1,lastBaseIndex + 1):
outData.append(str(index))
for anno in inData:
start = anno[1]
end = anno[2]
for index in range(start - 1,end):
outData [index] += '\t' + anno[0]
#########################################################################################################################
###Out file writing and saveing procedures###############################################################################
savePath += os.path.basename(inPath)[:-4] + '_byBase.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 + '\n')
outHandle.close()
if printOut: #if the -p modifier is supplied
for line in outData: #prints every line to the standard output...
print line
#########################################################################################################################
###Debug Saving procedures###############################################################################################
if saveDebug: #if the -d modifier is supplied...
DebugSavePath = savePath[:-4] + '.BADebug.txt' #the path to where the debug log is to be saved
debugHandle = open(fileSavePath, 'w') #opens the file object for saving the debug log
for line in debugLog:
debugHandle.write(line)
debugHandle.close()
#########################################################################################################################
