--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Protein_report_processing.py	Tue Aug 23 18:55:17 2016 -0400
@@ -0,0 +1,213 @@
+import sys
+import os
+from time import sleep
+
+files = sys.argv[1] # read in a string of file names seperated by ", "
+# e.g. "Default_Protein_Report.txt, Default_Protein_Report_2.txt"
+#bait = sys.argv[2] # SAINT formatted bait file
+# still need a way to match files to bait identifiers
+# or they can just be required to be put in the order of the bait file
+quant_type = sys.argv[3] # what metric to use for quantification
+# "#Validated Peptides", "#Peptides", "#Unique", "#Validated PSMs", "#PSMs"
+db = sys.argv[4] # fasta database used in SearchGUI and PeptideShaker
+prey = sys.argv[5]
+tool_path = sys.argv[7]
+if fasta_db == "None":
+    fasta_db = str(tool_path)  + "/SwissProt_HUMAN_2015_12.fasta"
+make_bait = sys.argv[6]
+bait_bool = sys.argv[8]
+
+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"
+
+class ReturnValue1(object):
+    def __init__(self, sequence, gene):
+        self.seqlength = sequence
+        self.genename = gene
+
+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
+    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())
+                        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())
+                    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 concatenate_files(file_list_string, bait_file):
+    file_list = file_list_string.split(", ")
+    bait = read_tab(bait_file)
+    master_table = []
+    header_check = 0
+    file_cnt = 0
+    table_cnt = 0
+    for i in file_list:
+        table = read_tab(i)
+        for j in table:
+            if table_cnt == 0:
+                if header_check == 0:
+                    header_check +=1
+                    j.append("Replicate")
+                    j.append("Bait_Grouping")
+                    master_table.append(j)
+            if table_cnt > 0:
+                j.append(bait[file_cnt][0])
+                j.append(bait[file_cnt][1])
+                master_table.append(j)
+            table_cnt +=1
+        file_cnt+=1
+        table_cnt = 0
+    if len(master_table[0]) < len(master_table[1]):
+        master_table[0] = ["#"] + master_table[0]
+    with open("merged_PeptideShaker.txt","w") as x:
+        for i in master_table:
+            x.write("\t".join(i))
+            x.write("\n")
+    return master_table
+def make_inter(master_table,quant_type):
+    if len(master_table[0]) < len(master_table[1]):
+        master_table[0] = ["#"] + master_table[0]
+    replicate_index = master_table[0].index("Replicate")
+    grouping_index = master_table[0].index("Bait_Grouping")
+    accession_index = master_table[0].index("Main Accession")
+    Quant_index = master_table[0].index(quant_type)
+    inter_file = ""
+    for i in master_table[1:]:
+        line = []
+        line.append(i[replicate_index])
+        line.append(i[grouping_index])
+        line.append(i[accession_index])
+        line.append(i[Quant_index])
+        inter_file = inter_file + "\t".join(line) + "\n"
+    with open("inter.txt","w") as x:
+        x.write(inter_file)
+    
+def make_prey(concat_table,fasta_db):
+    input_data = concat_table
+    if len(input_data[0]) < len(input_data[1]):
+        input_data[0] = ["#"] + input_data[0]
+    accession_index = input_data[0].index("Main Accession")
+    proteins = []
+    for i in input_data[1:]:
+        proteins.append(i[accession_index])
+    output_file = open("prey.txt", 'w')
+    start = 0
+    end = len(proteins)
+
+    # Initial call to print 0% progress
+    printProgress(start, end, prefix = 'Progress:', suffix = 'Complete', barLength = 50)
+
+    for protein in proteins:
+        seq = get_info(protein,fasta_db).seqlength
+        GN = get_info(protein,fasta_db).genename
+        if seq != 'NA':
+            output_file.write(protein + "\t" + str(seq) + "\t" + str(GN) + "\n")
+        start+=1
+        printProgress(start, end, prefix = 'Progress:', suffix = 'Complete', barLength = 50)
+    output_file.close()
+data = concatenate_files(files,bait)
+make_inter(data, quant_type)
+if prey == "true":
+    make_prey(data,db)
+
+os.rename("bait.txt", sys.argv[2])
+os.rename("inter.txt", sys.argv[10])
+os.rename("prey.txt", sys.argv[11])
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