import click

@click.command()
@click.argument('mirandafile')
@click.argument('output')
@click.option('-stop', default=20, help='''
Limits processing to the specified number of SNP entries\n
Parameter only used if debug is flagged\n
Default: 20\n
''')
@click.option('--debug', is_flag=True, help='Show debug messages')
def cli(mirandafile, output, stop, debug):

	"""
	\b
	Arguments:
		MIRANDAFILE - INPUT processed final output from firstpass script
		OUTPUT - fully processed first pass miRanda output
	
	Parses a miranda output file for a given chromosome and only retains 
	entries that have at least one, but not all, SNP alleles for a given 
	SNP ID in the upper 80th percentile."""

	try:
		parsemir(mirandafile, output, stop, debug)
		print("Success")
	except:
		print("Error")

def parsemir(mirandaOut, outputFile, stop, d):
	print("Processing first pass miranda output file")
	
	snp = None # SNP container 
	snpInfo = None # SNP ref info
	snpID = "default" # SNP ID
	snpTot = 0 # Total number of SNP alleles
	count = 1
	
	with open(mirandaOut) as f, open(outputFile, "w") as o:
		for line in f:
			if line[0]==">":
				# Data line 
				if d:
					toPrint = "Count number: " + str(count)
					print(toPrint)
					print(line)
				
				lineSplit = line.split("\t") # Split data line by tabs
				
				if d:
					print(lineSplit)
				
				snpInfo = lineSplit[1].split("|") # Split the SNP entry ID
				cmpID = snpInfo[2] # Use the rs number from the SNP entry ID 
				
				if d:
					toPrint = "Compare ID: " + cmpID
					print(toPrint)
					toPrint = "SNP ID: " + snpID
					print(toPrint)
				
				if snpID != cmpID:
					if snp != None:
						# For every case except the start 
						snpNum = len(snp) # Count number of SNP alleles in output 
						
						if d:
							toPrint = "SNP Alleles: " + str(snpNum) + "\nTotal Alleles: " + str(snpTot)
							print(toPrint)
						
						# Compare to total number of SNP alleles 
						if snpNum < snpTot: 
							# Print to file 
							if d:
								print("Printing previous SNPs:")
							
							for entry in snp:
								print("{}".format(entry), file=o)
								
								if d:
									print(entry)
						
					# Start new SNP container and info 
					snp = [line.replace("\n", "")]
					snpID = cmpID # Set snpID to the new rs number
					snpTot = int(snpInfo[3]) # Get new total num of alleles 
					
				else: 
					if d:
						print("Appending SNP line to container")
					
					snp.append(line.replace("\n", ""))
				
				if d:
					print("\nEnd of line")
					print("\n")
					print("\n")
					
					if count%stop==0:
						return
					
					count += 1
					
			elif line[0]=="#":
				if line[0:5]=="# End":
					# Compare SNP alleles for the last SNP container 
					snpNum = len(snp)
					snpTot = int(snpInfo[3])
					
					if snpNum < snpTot:
						# Print to file 
						for entry in snp:
							print("{}".format(entry), file=o)
							
				# Comment line, append to output file
				print("{}".format(line.replace("\n", "")), file=o)
da01ba4187dfc8564e6ab83d92a87038d6e4e67d
<mask token>

<mask token>


@click.command()
@click.argument('mirandafile')
@click.argument('output')
@click.option('-stop', default=20, help=
    """
Limits processing to the specified number of SNP entries

Parameter only used if debug is flagged

Default: 20

"""
    )
@click.option('--debug', is_flag=True, help='Show debug messages')
def cli(mirandafile, output, stop, debug):
    """
	
	Arguments:
		MIRANDAFILE - INPUT processed final output from firstpass script
		OUTPUT - fully processed first pass miRanda output
	
	Parses a miranda output file for a given chromosome and only retains 
	entries that have at least one, but not all, SNP alleles for a given 
	SNP ID in the upper 80th percentile."""
    try:
        parsemir(mirandafile, output, stop, debug)
        print('Success')
    except:
        print('Error')


<mask token>

<mask token>


@click.command()
@click.argument('mirandafile')
@click.argument('output')
@click.option('-stop', default=20, help=
    """
Limits processing to the specified number of SNP entries

Parameter only used if debug is flagged

Default: 20

"""
    )
@click.option('--debug', is_flag=True, help='Show debug messages')
def cli(mirandafile, output, stop, debug):
    """
	
	Arguments:
		MIRANDAFILE - INPUT processed final output from firstpass script
		OUTPUT - fully processed first pass miRanda output
	
	Parses a miranda output file for a given chromosome and only retains 
	entries that have at least one, but not all, SNP alleles for a given 
	SNP ID in the upper 80th percentile."""
    try:
        parsemir(mirandafile, output, stop, debug)
        print('Success')
    except:
        print('Error')


def parsemir(mirandaOut, outputFile, stop, d):
    print('Processing first pass miranda output file')
    snp = None
    snpInfo = None
    snpID = 'default'
    snpTot = 0
    count = 1
    with open(mirandaOut) as f, open(outputFile, 'w') as o:
        for line in f:
            if line[0] == '>':
                if d:
                    toPrint = 'Count number: ' + str(count)
                    print(toPrint)
                    print(line)
                lineSplit = line.split('\t')
                if d:
                    print(lineSplit)
                snpInfo = lineSplit[1].split('|')
                cmpID = snpInfo[2]
                if d:
                    toPrint = 'Compare ID: ' + cmpID
                    print(toPrint)
                    toPrint = 'SNP ID: ' + snpID
                    print(toPrint)
                if snpID != cmpID:
                    if snp != None:
                        snpNum = len(snp)
                        if d:
                            toPrint = 'SNP Alleles: ' + str(snpNum
                                ) + '\nTotal Alleles: ' + str(snpTot)
                            print(toPrint)
                        if snpNum < snpTot:
                            if d:
                                print('Printing previous SNPs:')
                            for entry in snp:
                                print('{}'.format(entry), file=o)
                                if d:
                                    print(entry)
                    snp = [line.replace('\n', '')]
                    snpID = cmpID
                    snpTot = int(snpInfo[3])
                else:
                    if d:
                        print('Appending SNP line to container')
                    snp.append(line.replace('\n', ''))
                if d:
                    print('\nEnd of line')
                    print('\n')
                    print('\n')
                    if count % stop == 0:
                        return
                    count += 1
            elif line[0] == '#':
                if line[0:5] == '# End':
                    snpNum = len(snp)
                    snpTot = int(snpInfo[3])
                    if snpNum < snpTot:
                        for entry in snp:
                            print('{}'.format(entry), file=o)
                print('{}'.format(line.replace('\n', '')), file=o)

import click


@click.command()
@click.argument('mirandafile')
@click.argument('output')
@click.option('-stop', default=20, help=
    """
Limits processing to the specified number of SNP entries

Parameter only used if debug is flagged

Default: 20

"""
    )
@click.option('--debug', is_flag=True, help='Show debug messages')
def cli(mirandafile, output, stop, debug):
    """
	
	Arguments:
		MIRANDAFILE - INPUT processed final output from firstpass script
		OUTPUT - fully processed first pass miRanda output
	
	Parses a miranda output file for a given chromosome and only retains 
	entries that have at least one, but not all, SNP alleles for a given 
	SNP ID in the upper 80th percentile."""
    try:
        parsemir(mirandafile, output, stop, debug)
        print('Success')
    except:
        print('Error')


def parsemir(mirandaOut, outputFile, stop, d):
    print('Processing first pass miranda output file')
    snp = None
    snpInfo = None
    snpID = 'default'
    snpTot = 0
    count = 1
    with open(mirandaOut) as f, open(outputFile, 'w') as o:
        for line in f:
            if line[0] == '>':
                if d:
                    toPrint = 'Count number: ' + str(count)
                    print(toPrint)
                    print(line)
                lineSplit = line.split('\t')
                if d:
                    print(lineSplit)
                snpInfo = lineSplit[1].split('|')
                cmpID = snpInfo[2]
                if d:
                    toPrint = 'Compare ID: ' + cmpID
                    print(toPrint)
                    toPrint = 'SNP ID: ' + snpID
                    print(toPrint)
                if snpID != cmpID:
                    if snp != None:
                        snpNum = len(snp)
                        if d:
                            toPrint = 'SNP Alleles: ' + str(snpNum
                                ) + '\nTotal Alleles: ' + str(snpTot)
                            print(toPrint)
                        if snpNum < snpTot:
                            if d:
                                print('Printing previous SNPs:')
                            for entry in snp:
                                print('{}'.format(entry), file=o)
                                if d:
                                    print(entry)
                    snp = [line.replace('\n', '')]
                    snpID = cmpID
                    snpTot = int(snpInfo[3])
                else:
                    if d:
                        print('Appending SNP line to container')
                    snp.append(line.replace('\n', ''))
                if d:
                    print('\nEnd of line')
                    print('\n')
                    print('\n')
                    if count % stop == 0:
                        return
                    count += 1
            elif line[0] == '#':
                if line[0:5] == '# End':
                    snpNum = len(snp)
                    snpTot = int(snpInfo[3])
                    if snpNum < snpTot:
                        for entry in snp:
                            print('{}'.format(entry), file=o)
                print('{}'.format(line.replace('\n', '')), file=o)

import click

@click.command()
@click.argument('mirandafile')
@click.argument('output')
@click.option('-stop', default=20, help='''
Limits processing to the specified number of SNP entries\n
Parameter only used if debug is flagged\n
Default: 20\n
''')
@click.option('--debug', is_flag=True, help='Show debug messages')
def cli(mirandafile, output, stop, debug):

	"""
	\b
	Arguments:
		MIRANDAFILE - INPUT processed final output from firstpass script
		OUTPUT - fully processed first pass miRanda output
	
	Parses a miranda output file for a given chromosome and only retains 
	entries that have at least one, but not all, SNP alleles for a given 
	SNP ID in the upper 80th percentile."""

	try:
		parsemir(mirandafile, output, stop, debug)
		print("Success")
	except:
		print("Error")

def parsemir(mirandaOut, outputFile, stop, d):
	print("Processing first pass miranda output file")
	
	snp = None # SNP container 
	snpInfo = None # SNP ref info
	snpID = "default" # SNP ID
	snpTot = 0 # Total number of SNP alleles
	count = 1
	
	with open(mirandaOut) as f, open(outputFile, "w") as o:
		for line in f:
			if line[0]==">":
				# Data line 
				if d:
					toPrint = "Count number: " + str(count)
					print(toPrint)
					print(line)
				
				lineSplit = line.split("\t") # Split data line by tabs
				
				if d:
					print(lineSplit)
				
				snpInfo = lineSplit[1].split("|") # Split the SNP entry ID
				cmpID = snpInfo[2] # Use the rs number from the SNP entry ID 
				
				if d:
					toPrint = "Compare ID: " + cmpID
					print(toPrint)
					toPrint = "SNP ID: " + snpID
					print(toPrint)
				
				if snpID != cmpID:
					if snp != None:
						# For every case except the start 
						snpNum = len(snp) # Count number of SNP alleles in output 
						
						if d:
							toPrint = "SNP Alleles: " + str(snpNum) + "\nTotal Alleles: " + str(snpTot)
							print(toPrint)
						
						# Compare to total number of SNP alleles 
						if snpNum < snpTot: 
							# Print to file 
							if d:
								print("Printing previous SNPs:")
							
							for entry in snp:
								print("{}".format(entry), file=o)
								
								if d:
									print(entry)
						
					# Start new SNP container and info 
					snp = [line.replace("\n", "")]
					snpID = cmpID # Set snpID to the new rs number
					snpTot = int(snpInfo[3]) # Get new total num of alleles 
					
				else: 
					if d:
						print("Appending SNP line to container")
					
					snp.append(line.replace("\n", ""))
				
				if d:
					print("\nEnd of line")
					print("\n")
					print("\n")
					
					if count%stop==0:
						return
					
					count += 1
					
			elif line[0]=="#":
				if line[0:5]=="# End":
					# Compare SNP alleles for the last SNP container 
					snpNum = len(snp)
					snpTot = int(snpInfo[3])
					
					if snpNum < snpTot:
						# Print to file 
						for entry in snp:
							print("{}".format(entry), file=o)
							
				# Comment line, append to output file
				print("{}".format(line.replace("\n", "")), file=o)