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1 # -*- coding: utf-8 -*-
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2 """
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3 Python-code: Preprocess mzIdentML
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4 @author = Brent Kuenzi
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5 @email = Brent.Kuenzi@moffitt.org
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6 """
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7 #######################################################################################
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8 ## Description: ##
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9 # This program will create inter, prey, and bait files from mzIdentML files
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10 ## Required input: ##
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11 # 1) mzIdentML file to be reformatted
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12 # 2) minimum PSM for quantification
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13
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14
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15 import sys
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16 import os
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17
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18 ins_path = sys.argv[5]
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19
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20 class ReturnValue1(object):
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21 def __init__(self, sequence, gene):
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22 self.seqlength = sequence
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23 self.genename = gene
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24 class ReturnValue2(object):
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25 def __init__(self, inter, accessions):
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26 self.inter = inter
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27 self.accessions = accessions
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28 def read_tab(infile):
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29 with open(infile,'r') as x:
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30 output = []
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31 for line in x:
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32 line = line.strip()
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33 temp = line.split('\t')
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34 output.append(temp)
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35 return output
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36 def printProgress (iteration, total, prefix = '', suffix = '', decimals = 1, barLength = 100):
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37 """
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38 Call in a loop to create terminal progress bar
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39 @params:
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40 iteration - Required : current iteration (Int)
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41 total - Required : total iterations (Int)
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42 prefix - Optional : prefix string (Str)
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43 suffix - Optional : suffix string (Str)
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44 decimals - Optional : positive number of decimals in percent complete (Int)
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45 barLength - Optional : character length of bar (Int)
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46 """
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47 formatStr = "{0:." + str(decimals) + "f}"
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48 percents = formatStr.format(100 * (iteration / float(total)))
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49 filledLength = int(round(barLength * iteration / float(total)))
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50 bar = '=' * filledLength + '-' * (barLength - filledLength)
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51 sys.stdout.write('\r%s |%s| %s%s %s' % (prefix, bar, percents, '%', suffix)),
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52 sys.stdout.flush()
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53 if iteration == total:
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54 sys.stdout.write('\n')
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55 sys.stdout.flush()
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56 def get_info(uniprot_accession_in,fasta_db):
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57 # Get aminoacid lengths and gene name.
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58 error = open('error proteins.txt', 'a+')
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59 data = open(fasta_db, 'r')
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60 data_lines = data.readlines()
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61 db_len = len(data_lines)
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62 seqlength = 0
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63 count = 0
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64 last_line = data_lines[-1]
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65 for data_line in data_lines:
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66 if ">sp" in data_line:
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67 namer = data_line.split("|")[2]
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68 if uniprot_accession_in == data_line.split("|")[1]:
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69 match = count + 1
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70 if 'GN=' in data_line:
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71 lst = data_line.split('GN=')
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72 lst2 = lst[1].split(' ')
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73 genename = lst2[0]
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74 if 'GN=' not in data_line:
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75 genename = 'NA'
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76 while ">sp" not in data_lines[match]:
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77 if match <= db_len:
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78 seqlength = seqlength + len(data_lines[match].strip())
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79 if data_lines[match] == last_line:
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80 break
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81 match = match + 1
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82 else:
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83 break
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84 return ReturnValue1(seqlength, genename)
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85 if uniprot_accession_in == namer.split(" ")[0]:
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86 match = count + 1
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87 # Ensures consistent spacing throughout.
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88 if 'GN=' in data_line:
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89 lst = data_line.split('GN=')
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90 lst2 = lst[1].split(' ')
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91 genename = lst2[0]
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92 if 'GN=' not in data_line:
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93 genename = 'NA'
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94 while ">sp" not in data_lines[match]:
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95 if match <= db_len:
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96 seqlength = seqlength + len(data_lines[match].strip())
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97 if data_lines[match] == last_line:
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98 break
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99 match = match + 1
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100 else:
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101 break
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102 return ReturnValue1(seqlength, genename)
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103 count = count + 1
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104 if seqlength == 0:
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105 error.write(uniprot_accession_in + '\t' + "Uniprot not in Fasta" + '\n')
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106 error.close
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107 seqlength = 'NA'
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108 genename = 'NA'
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109 return ReturnValue1(seqlength, genename)
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110 def make_inter(mzIdentML,replicate,grouping):
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111 accession_index = mzIdentML[0].index("accession")
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112 PSMs = {}
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113 accessions = []
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114 cnt = 0
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115 unique_lines = [mzIdentML[1:]]
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116 for i in mzIdentML[1:]:
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117 PSMs[i[accession_index]] = 0
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118 if i[accession_index] not in accessions:
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119 accessions.append(i[accession_index])
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120 if i not in unique_lines:
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121 unique_lines.append(i)
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122 for i in accessions:
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123 for j in unique_lines[1:]:
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124 if j[accession_index] == i:
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125 PSMs[j[accession_index]] +=1
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126 inter = ""
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127 for i in accessions:
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128 inter = inter + replicate + "\t" + grouping + "\t" + i + "\t" + str(PSMs[i]) + "\n"
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129 return ReturnValue2(inter,accessions)
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130
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131
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132 files = sys.argv[1]
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133 file_list = files.split(",")
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68
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134
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135 make_prey = sys.argv[3]
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136 db = sys.argv[4]
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137 if db == "None":
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138 db = str(ins_path) + "/SwissProt_HUMAN_2015_12.fasta"
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139 make_bait = sys.argv[6]
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140 bait_bool = sys.argv[7]
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141 prey_file = sys.argv[8]
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142 bait_out = sys.argv[9]
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143 inter_out = sys.argv[10]
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144
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145 def bait_create(baits, infile):
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146 # Verifies the Baits are valid in the Scaffold file and writes the Bait.txt.
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147 baits = make_bait.split()
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148 i = 0
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149 bait_file_tmp = open("bait.txt", "w")
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150 order = []
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151 bait_cache = []
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152 while i < len(baits):
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153 if baits[i+2] == "true":
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154 T_C = "C"
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155 else:
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156 T_C = "T"
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157 bait_line = baits[i] + "\t" + baits[i+1] + "\t" + T_C + "\n"
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158 bait_cache.append(str(bait_line))
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159 i = i + 3
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160
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161 for cache_line in bait_cache:
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162 bait_file_tmp.write(cache_line)
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163
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164 bait_file_tmp.close()
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165
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166 if bait_bool == 'false':
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167 bait_create(make_bait, infile)
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168 bait = "bait.txt"
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169 else:
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67
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170 bait_temp_file = open(sys.argv[2], 'r')
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171 bait_cache = bait_temp_file.readlines()
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172 bait_file_tmp = open("bait.txt", "wr")
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173 for cache_line in bait_cache:
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174 bait_file_tmp.write(cache_line)
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175 bait_file_tmp.close()
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176 bait = "bait.txt"
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177 bait = read_tab("bait.txt")
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178
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179 inter = ""
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180 cnt = 0
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181 accessions = []
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182 for i in file_list:
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183 cmd = (r"Rscript "+ str(ins_path) +"flatten_mzIdentML.R " + i)
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184 os.system(cmd)
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185 mzIdentML = read_tab("flat_mzIdentML.txt")
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186 inter = inter + make_inter(mzIdentML,bait[cnt][0],bait[cnt][1]).inter
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187 accessions.append(make_inter(mzIdentML,bait[cnt][0],bait[cnt][1]).accessions)
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188 cnt+=1
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189
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190 with open("inter.txt","w") as x:
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191 x.write(inter)
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192 if make_prey == "Y":
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193 unique_accessions = []
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194 prey = ""
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195 for i in accessions:
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196 for j in i:
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197 if j not in unique_accessions:
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198 unique_accessions.append(j)
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199 start = 0
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200 end = len(unique_accessions)
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201 printProgress(start,end,prefix = "Making Prey File:",suffix = "Complete",barLength=50)
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202
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203 for i in unique_accessions:
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204 prey = prey + i + "\t" + str(get_info(i,db).seqlength) + "\t" + get_info(i,db).genename + "\n"
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205 start+=1
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206 printProgress(start, end)
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207 with open("prey.txt","w") as x:
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208 x.write(prey)
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209
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210 os.rename("bait.txt", sys.argv[2])
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211 os.rename("inter.txt", sys.argv[10])
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212 if str(prey) != "None":
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213 os.rename("prey.txt", sys.argv[11]) |
