--- a/Protein_report_processing.py	Sat Aug 27 23:57:34 2016 -0400
+++ b/Protein_report_processing.py	Fri Sep 02 16:32:26 2016 -0400
@@ -1,221 +0,0 @@
-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 db == "None":
-    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
-    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 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_type = quant_type.replace("_", " ")
-    quant_type = r"#" + quant_type
-    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])
-if str(prey) != "None": 
-    os.rename("prey.txt", sys.argv[11])
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