--- a/mzID_process2.py	Sat Aug 27 23:22:20 2016 -0400
+++ b/mzID_process2.py	Sat Aug 27 23:26:10 2016 -0400
@@ -6,7 +6,7 @@
 """
 #######################################################################################
 ## Description: ##
-#    This program will create inter, prey, and bait files from mzIdentML files
+#This program will create inter, prey, and bait files from mzIdentML files
 ## Required input: ##
 # 1) mzIdentML file to be reformatted
 # 2) minimum PSM for quantification
@@ -18,95 +18,95 @@
 ins_path = sys.argv[5]
 
 class ReturnValue1(object):
-    def __init__(self, sequence, gene):
-        self.seqlength = sequence
-        self.genename = gene
+	def __init__(self, sequence, gene):
+		self.seqlength = sequence
+		self.genename = gene
 class ReturnValue2(object):
-    def __init__(self, inter, accessions):
-        self.inter = inter
-        self.accessions = accessions
+	def __init__(self, inter, accessions):
+		self.inter = inter
+		self.accessions = accessions
 def read_tab(infile):
-    with open(infile,'r') as x:
-        output = []
-        for line in x:
-            line = line.strip()
-            temp = line.split('\t')
-            output.append(temp)
-    return output
+	with open(infile,'r') as x:
+		output = []
+		for line in x:
+			line = line.strip()
+			temp = line.split('\t')
+			output.append(temp)
+	return output
 def printProgress (iteration, total, prefix = '', suffix = '', decimals = 1, barLength = 100):
-    """
-    Call in a loop to create terminal progress bar
-    @params:
-        iteration   - Required  : current iteration (Int)
-        total       - Required  : total iterations (Int)
-        prefix      - Optional  : prefix string (Str)
-        suffix      - Optional  : suffix string (Str)
-        decimals    - Optional  : positive number of decimals in percent complete (Int)
-        barLength   - Optional  : character length of bar (Int)
-    """
-    formatStr       = "{0:." + str(decimals) + "f}"
-    percents        = formatStr.format(100 * (iteration / float(total)))
-    filledLength    = int(round(barLength * iteration / float(total)))
-    bar             = '=' * filledLength + '-' * (barLength - filledLength)
-    sys.stdout.write('\r%s |%s| %s%s %s' % (prefix, bar, percents, '%', suffix)),
-    sys.stdout.flush()
-    if iteration == total:
-        sys.stdout.write('\n')
-        sys.stdout.flush()
+	"""
+	Call in a loop to create terminal progress bar
+	@params:
+		iteration   - Required  : current iteration (Int)
+		total	   - Required  : total iterations (Int)
+		prefix	  - Optional  : prefix string (Str)
+		suffix	  - Optional  : suffix string (Str)
+		decimals	- Optional  : positive number of decimals in percent complete (Int)
+		barLength   - Optional  : character length of bar (Int)
+	"""
+	formatStr	   = "{0:." + str(decimals) + "f}"
+	percents		= formatStr.format(100 * (iteration / float(total)))
+	filledLength	= int(round(barLength * iteration / float(total)))
+	bar			 = '=' * filledLength + '-' * (barLength - filledLength)
+	sys.stdout.write('\r%s |%s| %s%s %s' % (prefix, bar, percents, '%', suffix)),
+	sys.stdout.flush()
+	if iteration == total:
+		sys.stdout.write('\n')
+		sys.stdout.flush()
 def get_info(uniprot_accession_in,fasta_db): 
-    # Get aminoacid lengths and gene name.
-    error = open('error proteins.txt', 'a+')
-    data = open(fasta_db, 'r')
-    data_lines = data.readlines()
-    db_len = len(data_lines)
-    seqlength = 0
-    count = 0
-    last_line = data_lines[-1]
-    for data_line in data_lines:
-        if ">sp" in data_line:
-            namer = data_line.split("|")[2]
-            if uniprot_accession_in == data_line.split("|")[1]:
-                match = count + 1
-                if 'GN=' in data_line:
-                    lst = data_line.split('GN=')
-                    lst2 = lst[1].split(' ')
-                    genename = lst2[0]
-                if 'GN=' not in data_line:
-                    genename = 'NA'
-                while ">sp" not in data_lines[match]:
-                    if match <= db_len:
-                        seqlength = seqlength + len(data_lines[match].strip())
-                        if data_lines[match] == last_line:
-                            break
-                        match = match + 1
-                    else:
-                        break
-                return ReturnValue1(seqlength, genename)
-        if uniprot_accession_in == namer.split(" ")[0]:
-            match = count + 1
-            # Ensures consistent spacing throughout.
-            if 'GN=' in data_line:
-                lst = data_line.split('GN=')
-                lst2 = lst[1].split(' ')
-                genename = lst2[0]
-            if 'GN=' not in data_line:
-                genename = 'NA'
-            while ">sp" not in data_lines[match]:
-                if match <= db_len:
-                    seqlength = seqlength + len(data_lines[match].strip())
-                    if data_lines[match] == last_line:
-                        break
-                    match = match + 1
-                else:
-                    break
-            return ReturnValue1(seqlength, genename)
-        count = count + 1
-    if seqlength == 0:
-        error.write(uniprot_accession_in + '\t' + "Uniprot not in Fasta" + '\n')
-        error.close
-        seqlength = 'NA'
-        genename = 'NA'
-        return ReturnValue1(seqlength, genename)
+	# Get aminoacid lengths and gene name.
+	error = open('error proteins.txt', 'a+')
+	data = open(fasta_db, 'r')
+	data_lines = data.readlines()
+	db_len = len(data_lines)
+	seqlength = 0
+	count = 0
+	last_line = data_lines[-1]
+	for data_line in data_lines:
+		if ">sp" in data_line:
+			namer = data_line.split("|")[2]
+			if uniprot_accession_in == data_line.split("|")[1]:
+				match = count + 1
+				if 'GN=' in data_line:
+					lst = data_line.split('GN=')
+					lst2 = lst[1].split(' ')
+					genename = lst2[0]
+				if 'GN=' not in data_line:
+					genename = 'NA'
+				while ">sp" not in data_lines[match]:
+					if match <= db_len:
+						seqlength = seqlength + len(data_lines[match].strip())
+						if data_lines[match] == last_line:
+							break
+						match = match + 1
+					else:
+						break
+				return ReturnValue1(seqlength, genename)
+		if uniprot_accession_in == namer.split(" ")[0]:
+			match = count + 1
+			# Ensures consistent spacing throughout.
+			if 'GN=' in data_line:
+				lst = data_line.split('GN=')
+				lst2 = lst[1].split(' ')
+				genename = lst2[0]
+			if 'GN=' not in data_line:
+				genename = 'NA'
+			while ">sp" not in data_lines[match]:
+				if match <= db_len:
+					seqlength = seqlength + len(data_lines[match].strip())
+					if data_lines[match] == last_line:
+						break
+					match = match + 1
+				else:
+					break
+			return ReturnValue1(seqlength, genename)
+		count = count + 1
+	if seqlength == 0:
+		error.write(uniprot_accession_in + '\t' + "Uniprot not in Fasta" + '\n')
+		error.close
+		seqlength = 'NA'
+		genename = 'NA'
+		return ReturnValue1(seqlength, genename)
 def make_inter(mzIdentML,replicate,grouping):
 	accession_index = mzIdentML[0].index("accession")
 	PSMs = {}
@@ -135,7 +135,7 @@
 make_prey = sys.argv[3]
 db = sys.argv[4]
 if db == "None":
-    db = str(ins_path)  + "/SwissProt_HUMAN_2015_12.fasta"
+	db = str(ins_path)  + "/SwissProt_HUMAN_2015_12.fasta"
 make_bait = sys.argv[6]
 bait_bool = sys.argv[7]
 prey_file = sys.argv[8]
@@ -143,37 +143,37 @@
 inter_out = sys.argv[10]
 
 def bait_create(baits, infile):
-    # Verifies the Baits are valid in the Scaffold file and writes the Bait.txt.
-    baits = make_bait.split()
-    i = 0
-    bait_file_tmp = open("bait.txt", "w")
-    order = []
-    bait_cache = []
-    while i < len(baits):
-        if baits[i+2] == "true":
-            T_C = "C"
-        else:
-            T_C = "T"
-        bait_line = baits[i] + "\t" + baits[i+1] + "\t" + T_C + "\n"
-        bait_cache.append(str(bait_line))
-        i = i + 3
+	# Verifies the Baits are valid in the Scaffold file and writes the Bait.txt.
+	baits = make_bait.split()
+	i = 0
+	bait_file_tmp = open("bait.txt", "w")
+	order = []
+	bait_cache = []
+	while i < len(baits):
+		if baits[i+2] == "true":
+			T_C = "C"
+		else:
+			T_C = "T"
+		bait_line = baits[i] + "\t" + baits[i+1] + "\t" + T_C + "\n"
+		bait_cache.append(str(bait_line))
+		i = i + 3
 
-    for cache_line in bait_cache:
-        bait_file_tmp.write(cache_line)
+	for cache_line in bait_cache:
+		bait_file_tmp.write(cache_line)
 
-    bait_file_tmp.close()
+	bait_file_tmp.close()
 
 if bait_bool == 'false':
-    bait_create(make_bait, infile)
-    bait = "bait.txt"
+	bait_create(make_bait, infile)
+	bait = "bait.txt"
 else:
-    bait_temp_file = open(sys.argv[2], 'r')
-    bait_cache = bait_temp_file.readlines()
-    bait_file_tmp = open("bait.txt", "wr")
-    for cache_line in bait_cache:
-        bait_file_tmp.write(cache_line)
-    bait_file_tmp.close()
-    bait = "bait.txt"
+	bait_temp_file = open(sys.argv[2], 'r')
+	bait_cache = bait_temp_file.readlines()
+	bait_file_tmp = open("bait.txt", "wr")
+	for cache_line in bait_cache:
+		bait_file_tmp.write(cache_line)
+	bait_file_tmp.close()
+	bait = "bait.txt"
 bait = read_tab("bait.txt")
 
 inter = ""
@@ -184,9 +184,9 @@
 	os.system(cmd)
 	mzIdentML = read_tab("flat_mzIdentML.txt")
 	inter = inter + make_inter(mzIdentML,bait[cnt][0],bait[cnt][1]).inter
-    print inter
+	print inter
 	accessions.append(make_inter(mzIdentML,bait[cnt][0],bait[cnt][1]).accessions)
-    print accessions
+	print accessions
 	cnt+=1
 
 with open("inter.txt","w") as x:
@@ -205,11 +205,11 @@
 	for i in unique_accessions:
 		prey = prey + i + "\t" + str(get_info(i,db).seqlength) + "\t" + get_info(i,db).genename + "\n"
 		start+=1
-        printProgress(start, end)
+		printProgress(start, end)
 	with open("prey.txt","w") as x:
 		x.write(prey)
 
 os.rename("bait.txt", bait_out)
 os.rename("inter.txt", inter_out)
 if str(prey_file) != "None": 
-    os.rename("prey.txt", prey_file)
\ No newline at end of file
+	os.rename("prey.txt", prey_file)
\ No newline at end of file