--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mzID_process2.py	Sat Aug 27 22:13:31 2016 -0400
@@ -0,0 +1,212 @@
+# -*- coding: utf-8 -*-
+"""
+Python-code: Preprocess mzIdentML
+@author = Brent Kuenzi
+@email = Brent.Kuenzi@moffitt.org
+"""
+#######################################################################################
+## Description: ##
+#    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
+
+
+import sys
+import os
+
+ins_path = sys.argv[5]
+
+class ReturnValue1(object):
+    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 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
+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()
+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)
+def make_inter(mzIdentML,replicate,grouping):
+	accession_index = mzIdentML[0].index("accession")
+	PSMs = {}
+	accessions = []
+	cnt = 0
+	unique_lines = [mzIdentML[1:]]
+	for i in mzIdentML[1:]:
+		PSMs[i[accession_index]] = 0
+		if i[accession_index] not in accessions:
+			accessions.append(i[accession_index])
+		if i not in unique_lines:
+			unique_lines.append(i)
+	for i in accessions:
+		for j in unique_lines[1:]:
+			if j[accession_index] == i:
+				PSMs[j[accession_index]] +=1
+	inter = ""
+	for i in accessions:
+		inter = inter + replicate + "\t" + grouping + "\t" + i + "\t" + str(PSMs[i]) + "\n"
+	return ReturnValue2(inter,accessions)
+
+
+files = sys.argv[1]
+file_list = files.split(",")
+bait = read_tab(sys.argv[2])
+make_prey = sys.argv[3]
+db = sys.argv[4]
+if db == "None":
+    db = str(ins_path)  + "/SwissProt_HUMAN_2015_12.fasta"
+make_bait = sys.argv[6]
+bait_bool = sys.argv[7]
+prey_file = sys.argv[8]
+bait_out = sys.argv[9]
+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
+
+    for cache_line in bait_cache:
+        bait_file_tmp.write(cache_line)
+
+    bait_file_tmp.close()
+
+if bait_bool == 'false':
+    bait_create(make_bait, infile)
+    bait = "bait.txt"
+else:
+    bait_temp_file = open(sys.argv[9], '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"
+
+inter = ""
+cnt = 0
+accessions = []
+for i in file_list:
+	cmd = (r"Rscript "+ str(ins_path) +"flatten_mzIdentML.R " + i)
+	os.system(cmd)
+	mzIdentML = read_tab("flat_mzIdentML.txt")
+	inter = inter + make_inter(mzIdentML,bait[cnt][0],bait[cnt][1]).inter
+	accessions.append(make_inter(mzIdentML,bait[cnt][0],bait[cnt][1]).accessions)
+	cnt+=1
+
+with open("inter.txt","w") as x:
+	x.write(inter)
+if make_prey == "Y":
+	unique_accessions = []
+	prey = ""
+	for i in accessions:
+		for j in i:
+			if j not in unique_accessions:
+				unique_accessions.append(j)
+	start = 0
+	end = len(unique_accessions)
+	printProgress(start,end,prefix = "Making Prey File:",suffix = "Complete",barLength=50)
+
+	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)
+	with open("prey.txt","w") as x:
+		x.write(prey)
+
+os.rename("bait.txt", sys.argv[2])
+os.rename("inter.txt", sys.argv[10])
+if str(prey) != "None": 
+    os.rename("prey.txt", sys.argv[11])
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