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1 #######################################################################################
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2 # Python-code: SAINT pre-processing from maxquant "Samples Report" output
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3 # Author: Brent Kuenzi
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4 #######################################################################################
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5 # This program reads in a raw maxquant "Samples Report" output and a user generated
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6 # bait file and autoformats it into prey and interaction files for SAINTexpress
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7 # analysis
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8 #######################################################################################
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9 import sys
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10 import urllib2
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11 import os
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12 #######################################################################################
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13 ## REQUIRED INPUT ##
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14
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15 # 1) infile: maxquant "Samples Report" output
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16 # 2) baitfile: SAINT formatted bait file generated in Galaxy
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17 # 3) prey: Y or N for generating a prey file (requires internet connection)
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18 #######################################################################################
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19 mq_file = sys.argv[1]
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20 cmd = r"Rscript /home/bornea/galaxy_moffitt_dev/tools/Moffitt_Tools/bubblebeam/pre_process_protein_name_set.R " + str(mq_file)
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21 os.system(cmd)
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22
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23 infile = "./tukeys_output.txt" #maxquant "Samples Report" output
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24 prey = sys.argv[2] # Y or N
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25 fasta_db = sys.argv[3]
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26 if fasta_db == "None":
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27 fasta_db = "/home/bornea/galaxy_moffitt_dev/tools/Moffitt_Tools/bubblebeam/SwissProt_HUMAN_2014_08.fasta"
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28 make_bait= sys.argv[6]
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29
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30 def bait_create(baits, infile):
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31 #Takes the Bait specified by the user and makes them into a Bait file and includes a check to make sure they are using valid baits.
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32 baits = make_bait.split()
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33 i = 0
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34 bait_file_tmp = open("bait.txt", "wr")
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35 order = []
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36 bait_cache = []
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37 while i < len(baits):
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38 if baits[i+2] == "true":
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39 T_C = "C"
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40 else:
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41 T_C = "T"
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42 line1 = baits[i] + "\t" + baits[i+1] + "\t" + T_C + "\n"
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43 q = open(infile,"r")
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44 for line2 in q:
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45 line2 = line2.replace("\"", "")
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46 line2 = line2.replace(r"Intensity.", "") #R coerces "-" into "." this changes them back and remove Intensity from the Bait names.
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47 line2 = line2.replace(r".", r"-")
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48 temp = line2.split()
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49 if "mapped_protein" in str(temp):
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50 #If the bait is in the original file then write to cache it if not exit.
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51 if baits[i] in temp:
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52 number_bait = temp.index(str(baits[i]))
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53 number_bait = number_bait - 9
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54 bait_cache.append((number_bait, str(line1)))
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55 else:
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56 print "Error: bad bait " + str(baits[i])
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57 sys.exit()
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58 else:
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59 pass
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60 i = i + 3
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61 #Writes cache to file.
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62 bait_cache.sort()
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63 for line in bait_cache:
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64 bait_file_tmp.write(line[1])
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65
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66 bait_file_tmp.close()
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67
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68
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69 baitfile = "bait.txt"
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70
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71 class ReturnValue1(object):
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72 def __init__(self, sequence, gene):
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73 self.seqlength = sequence
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74 self.genename = gene
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75 class ReturnValue2(object):
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76 def __init__(self, getdata, getproteins, getheader):
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77 self.data = getdata
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78 self.proteins = getproteins
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79 self.header = getheader
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80
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81 def main(maxquant_input, make_bait):
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82 bait_create(make_bait, infile)
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83 baitfile = "bait.txt"
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84 #bait_check(baitfile, maxquant_input)
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85 make_inter(maxquant_input)
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86 if prey == 'true':
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87 make_prey(maxquant_input)
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88 no_error_inter(maxquant_input)
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89 os.rename('prey.txt', sys.argv[5])
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90 elif prey == 'false':
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91 if os.path.isfile('error proteins.txt') == True:
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92 no_error_inter(maxquant_input)
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93 pass
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94 elif prey != 'true' or 'false':
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95 sys.exit("Invalid Prey Argument: Y or N")
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96 os.rename('inter.txt', sys.argv[4])
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97 os.rename("bait.txt", sys.argv[7])
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98
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99
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100 def get_info(uniprot_accession_in): # get aa lengths and gene name
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101 error = open('error proteins.txt', 'a+')
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102 # while True:
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103 # i = 0
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104 # try:
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105 # data = urllib2.urlopen("http://www.uniprot.org/uniprot/" + uniprot_accession_in + ".fasta")
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106 # break
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107 # except urllib2.HTTPError, err:
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108 # i = i + 1
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109 # if i == 50:
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110 # sys.exit("More than 50 errors. Check your file or try again later.")
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111 # if err.code == 404:
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112 # error.write(uniprot_accession_in + '\t' + "Invalid URL. Check protein" + '\n')
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113 # seqlength = 'NA'
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114 # genename = 'NA'
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115 # return ReturnValue1(seqlength, genename)
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116 # elif err.code == 302:
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117 # sys.exit("Request timed out. Check connection and try again.")
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118 # else:
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119 # sys.exit("Uniprot had some other error")
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120 #
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121 #
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122 # if lines == []:
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123 # error.write(uniprot_accession_in + '\t' + "Blank Fasta" + '\n')
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124 # error.close
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125 # if lines == []:
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126 # error.write(uniprot_accession_in + '\t' + "Blank Fasta" + '\n')
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127 # error.close
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128 # seqlength = 'NA'
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129 # genename = 'NA'
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130 # return ReturnValue1(seqlength, genename)
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131 # if lines != []:
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132 # seqlength = 0
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133 # header = lines[0]
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134 # for line in lines[1:]:
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135 # line = line.replace("\n","") # strip \n or else it gets counted in the length
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136 # seqlength += len(line)
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137 # if 'GN=' in header:
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138 # lst = header.split('GN=')
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139 # lst2 = lst[1].split(' ')
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140 # genename = lst2[0]
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141 # error.close
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142 # return ReturnValue1(seqlength, genename)
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143 # if 'GN=' not in header:
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144 # genename = 'NA'
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145 # error.close
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146 # return ReturnValue1(seqlength, genename)
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147
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148 data = open(fasta_db,'r')
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149 lines = data.readlines()
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150 db_len = len(lines)
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151 seqlength = 0
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152 count = 0
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153 for i in lines:
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154 if ">sp" in i:
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155 if uniprot_accession_in == i.split("|")[1]:
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156 match = count+1
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157 if 'GN=' in i:
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158 lst = i.split('GN=')
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159 lst2 = lst[1].split(' ')
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160 genename = lst2[0]
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161 if 'GN=' not in i:
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162 genename = 'NA'
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163 while ">sp" not in lines[match]:
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164 if match <= db_len:
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165 seqlength = seqlength + len(lines[match].strip())
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166 match = match + 1
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167 else:
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168 break
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169 return ReturnValue1(seqlength, genename)
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170 count = count + 1
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171
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172
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173 if seqlength == 0:
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174 error.write(uniprot_accession_in + '\t' + "Uniprot not in Fasta" + '\n')
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175 error.close
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176 seqlength = 'NA'
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177 genename = 'NA'
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178 return ReturnValue1(seqlength, genename)
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179
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180
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181 def readtab(infile):
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182 with open(infile,'r') as x: # read in tab-delim text
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183 output = []
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184 for line in x:
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185 line = line.strip()
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186 temp = line.split('\t')
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187 output.append(temp)
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188 return output
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189 def read_maxquant(maxquant_input): # Get data, proteins and header from maxquant output
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190 dupes = readtab(maxquant_input)
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191 header_start = 0
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192 header = dupes[header_start]
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193 for i in header:
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194 i = i.replace(r"\"", "")
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195 i = i.replace(r"Intensity.", r"")
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196 i = i.replace(r".", r"-")
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197 data = dupes[header_start+1:len(dupes)] #cut off blank line and END OF FILE
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198 proteins = []
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199 for protein in data:
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200 proteins.append(protein[0])
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201 return ReturnValue2(data, proteins, header)
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202 def make_inter(maxquant_input):
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203 bait = readtab(baitfile)
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204 data = read_maxquant(maxquant_input).data
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205 header = read_maxquant(maxquant_input).header
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206 proteins = read_maxquant(maxquant_input).proteins
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207 bait_index = []
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208 for i in bait:
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209 bait_index.append(header.index("mapped_protein") + 1) # Find just the baits defined in bait file
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210 with open('inter.txt', 'w') as y:
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211 a = 0; l=0
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212 for bb in bait:
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213 for lst in data:
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214 y.write(header[bait_index[l]] + '\t' + bb[1] + '\t' + proteins[a] + '\t' + lst[bait_index[l]] + '\n')
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215 a+=1
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216 if a == len(proteins):
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217 a = 0; l+=1
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218 def make_prey(maxquant_input):
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219 proteins = read_maxquant(maxquant_input).proteins
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220 output_file = open("prey.txt",'w')
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221 for a in proteins:
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222 a = a.replace("\n","") # remove \n for input into function
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223 a = a.replace("\r","") # ditto for \r
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224 seq = get_info(a).seqlength
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225 GN = get_info(a).genename
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226 if seq != 'NA':
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227 output_file.write(a+"\t"+str(seq)+ "\t" + str(GN) + "\n")
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228 output_file.close()
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229 def no_error_inter(maxquant_input): # remake inter file without protein errors from Uniprot
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230 err = readtab("error proteins.txt")
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231 bait = readtab(baitfile)
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232 data = read_maxquant(maxquant_input).data
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233 header = read_maxquant(maxquant_input).header
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234 header = [i.replace(r"\"", "") for i in header]
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235 header = [i.replace(r"Intensity.", r"") for i in header]
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236 header = [i.replace(r".", r"-") for i in header]
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237 print header
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238 bait_index = []
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239 for i in bait:
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240 bait_index.append(header.index(i[0]))
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241 proteins = read_maxquant(maxquant_input).proteins
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242 errors = []
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243 for e in err:
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244 errors.append(e[0])
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245 with open('inter.txt', 'w') as y:
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246 l = 0; a = 0
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247 for bb in bait:
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248 for lst in data:
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249 if proteins[a] not in errors:
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250 y.write(header[bait_index[l]] + '\t' + bb[1] + '\t' + proteins[a] + '\t' + lst[bait_index[l]] + '\n')
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251 a+=1
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252 if a == len(proteins):
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253 l += 1; a = 0
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254 def bait_check(bait, maxquant_input): # check that bait names share header titles
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255 bait_in = readtab(bait)
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256 header = read_maxquant(maxquant_input).header
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257 for i in bait_in:
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258 if i[0] not in header:
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259 sys.exit("Bait must share header titles with maxquant output")
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260
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261 if __name__ == '__main__':
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262 main(infile, make_bait)
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