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1 #######################################################################################
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2 # Python-code: SAINT pre-processing from Scaffold "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 Scaffold "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 # Copyright (C) Brent Kuenzi.
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10 # Permission is granted to copy, distribute and/or modify this document
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11 # under the terms of the GNU Free Documentation License, Version 1.3
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12 # or any later version published by the Free Software Foundation;
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13 # with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
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14 # A copy of the license is included in the section entitled "GNU
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15 # Free Documentation License".
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16 #######################################################################################
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17 ## REQUIRED INPUT ##
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18
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19 # 1) infile: Scaffold "Samples Report" output
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20 # 2) baitfile: SAINT formatted bait file generated in Galaxy
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21 # 3) fasta_db: fasta database for use (defaults to SwissProt_HUMAN_2014_08.fasta)
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22 # 4) prey: Y or N for generating a prey file
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23 # 5) make_bait: String of bait names, assignment, and test or control boolean
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24 #######################################################################################
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25
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26 import sys
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27 import os.path
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28
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29
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30 infile = sys.argv[1]
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31 #Scaffold "Samples Report" output.
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32 prey = sys.argv[2]
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33 # Y or N boolean from Galaxy.
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34 fasta_db = sys.argv[3]
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35 tool_path = sys.argv[8]
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36 if fasta_db == "None":
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37 fasta_db = str(tool_path) + "/SwissProt_HUMAN_2014_08.fasta"
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38 make_bait = sys.argv[6]
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39 bait_bool = sys.argv[9]
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40
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41
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42 def bait_create(baits, infile):
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43 # Verifies the Baits are valid in the Scaffold file and writes the Bait.txt.
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44 baits = make_bait.split()
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45 i = 0
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46 bait_file_tmp = open("bait.txt", "w")
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47 order = []
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48 bait_cache = []
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49 while i < len(baits):
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50 if baits[i+2] == "true":
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51 T_C = "C"
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52 else:
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53 T_C = "T"
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54 bait_line = baits[i] + "\t" + baits[i+1] + "\t" + T_C + "\n"
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55 read_infile = open(infile, "r")
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56 for input_line in read_infile:
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57 input_line = input_line.strip()
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58 temp = input_line.split('\t')
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59 if "Quantitative Variance" in str(temp):
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60 if baits[i] in temp:
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61 number_bait = temp.index(str(baits[i]))
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62 number_bait = number_bait - 9
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63 bait_cache.append((number_bait, str(bait_line)))
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64 # Locates the Bait names in the column names and then sets the Baits in the
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65 # correct order in the cache thus the - 9 because the baits start at the 9th
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66 # column.
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67 else:
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68 print "Error: bad bait " + str(baits[i])
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69 sys.exit()
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70 else:
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71 pass
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72 i = i + 3
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73
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74 bait_cache.sort()
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75 for cache_line in bait_cache:
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76 bait_file_tmp.write(cache_line[1])
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77
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78 bait_file_tmp.close()
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79
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80 if bait_bool == 'false':
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81 bait_create(make_bait, infile)
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82 baitfile = "bait.txt"
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83 else:
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84 bait_temp_file = open(sys.argv[10], 'r')
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85 bait_cache = bait_temp_file.readlines()
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86 print bait_cache
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87 bait_file_tmp = open("bait.txt", "wr")
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88 for cache_line in bait_cache:
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89 bait_file_tmp.write(cache_line)
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90 bait_file_tmp.close()
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91 baitfile = "bait.txt"
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92
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93
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94 class ReturnValue1(object):
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95 def __init__(self, sequence, gene):
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96 self.seqlength = sequence
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97 self.genename = gene
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98
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99
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100 class ReturnValue2(object):
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101 def __init__(self, getdata, getproteins, getheader):
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102 self.data = getdata
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103 self.proteins = getproteins
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104 self.header = getheader
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105
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106
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107 def main(Scaffold_input, baits):
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108 bait_check(baitfile, Scaffold_input)
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109 make_inter(Scaffold_input)
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110 if prey == 'true':
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111 make_prey(Scaffold_input)
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112 no_error_inter(Scaffold_input)
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113 os.rename('prey.txt', sys.argv[5])
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114 elif prey == 'false':
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115 if os.path.isfile('error proteins.txt') == True:
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116 no_error_inter(Scaffold_input)
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117 pass
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118 elif prey != 'true' or 'false':
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119 sys.exit("Invalid Prey Argument: Y or N")
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120
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121
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122 def get_info(uniprot_accession_in):
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123 # Get aminoacid lengths and gene name.
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124 error = open('error proteins.txt', 'a+')
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125 data = open(fasta_db, 'r')
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126 data_lines = data.readlines()
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127 db_len = len(data_lines)
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128 seqlength = 0
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129 count = 0
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130 for data_line in data_lines:
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131 if ">sp" in data_line:
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132 namer = data_line.split("|")[2]
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133 if uniprot_accession_in == data_line.split("|")[1]:
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134 match = count + 1
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135 if 'GN=' in data_line:
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136 lst = data_linedata_line.split('GN=')
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137 lst2 = lst[1].split(' ')
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138 genename = lst2[0]
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139 if 'GN=' not in data_line:
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140 genename = 'NA'
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141 while ">sp" not in data_lines[match]:
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142 if match <= db_len:
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143 seqlength = seqlength + len(data_lines[match].strip())
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144 match = match + 1
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145 else:
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146 break
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147 return ReturnValue1(seqlength, genename)
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148 elif uniprot_accession_in == namer.split(" ")[0]:
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149 match = count + 1
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150 # Ensures consistent spacing throughout.
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151 if 'GN=' in data_line:
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152 lst = data_line.split('GN=')
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153 lst2 = lst[1].split(' ')
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154 genename = lst2[0]
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155 if 'GN=' not in data_line:
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156 genename = 'NA'
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157 while ">sp" not in lines[match]:
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158 if match <= db_len:
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159 seqlength = seqlength + len(lines[match].strip())
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160 match = match + 1
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161 else:
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162 break
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163 return ReturnValue1(seqlength, genename)
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164 count = count + 1
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165 if seqlength == 0:
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166 error.write(uniprot_accession_in + '\t' + "Uniprot not in Fasta" + '\n')
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167 error.close
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168 seqlength = 'NA'
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169 genename = 'NA'
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170 return ReturnValue1(seqlength, genename)
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171
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172
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173 def readtab(infile):
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174 with open(infile, 'r') as input_file:
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175 # read in tab-delim text
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176 output = []
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177 for input_line in input_file:
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178 input_line = input_line.strip()
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179 temp = input_line.split('\t')
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180 output.append(temp)
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181 return output
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182
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183
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184 def read_Scaffold(Scaffold_input):
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185 # Get data, proteins and header from Scaffold output
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186 dupes = readtab(Scaffold_input)
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187 cnt = 0
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188 for Scaffold_line in dupes:
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189 cnt += 1
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190 if Scaffold_line[0] == '#':
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191 # Finds the start of second header.
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192 header_start = cnt-1
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193 header = dupes[header_start]
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194 prot_start = header.index("Accession Number")
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195 data = dupes[header_start+1:len(dupes)-2]
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196 # Cut off blank line and END OF FILE.
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197 proteins = []
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198 for Scaffold_line in data:
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199 Scaffold_line[4] = Scaffold_line[4].split()[0]
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200 # Removes the (+##) that sometimes is attached.
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201 for protein in data:
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202 proteins.append(protein[prot_start])
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203 return ReturnValue2(data, proteins, header)
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204
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205
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206 def make_inter(Scaffold_input):
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207 bait = readtab(baitfile)
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208 data = read_Scaffold(Scaffold_input).data
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209 header = read_Scaffold(Scaffold_input).header
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210 proteins = read_Scaffold(Scaffold_input).proteins
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211 bait_index = []
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212 for bait_line in bait:
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213 bait_index.append(header.index(bait_line[0]))
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214 # Find just the baits defined in bait file.
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215 with open('inter.txt', 'w') as inter_file:
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216 a = 0; l = 0
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217 for bb in bait:
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218 for lst in data:
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219 inter_file.write(header[bait_index[l]] + '\t' + bb[1] + '\t' + proteins[a] + '\t'
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220 + lst[bait_index[l]] + '\n')
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221 a += 1
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222 if a == len(proteins):
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223 a = 0; l += 1
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224
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225
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226 def make_prey(Scaffold_input):
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227 proteins = read_Scaffold(Scaffold_input).proteins
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228 output_file = open("prey.txt", 'w')
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229 for protein in proteins:
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230 protein = protein.replace("\n", "")
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231 # Remove \n for input into function.
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232 protein = protein.replace("\r", "")
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233 # Ditto for \r.
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234 seq = get_info(protein).seqlength
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235 GN = get_info(protein).genename
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236 if seq != 'NA':
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237 output_file.write(protein + "\t" + str(seq) + "\t" + str(GN) + "\n")
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238 output_file.close()
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239
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240
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241 def no_error_inter(Scaffold_input):
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242 # Remake inter file without protein errors from Uniprot.
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243 err = readtab("error proteins.txt")
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244 bait = readtab(baitfile)
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245 data = read_Scaffold(Scaffold_input).data
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246 header = read_Scaffold(Scaffold_input).header
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247 bait_index = []
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248 for bait_line in bait:
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249 bait_index.append(header.index(bait_line[0]))
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250 proteins = read_Scaffold(Scaffold_input).proteins
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251 errors = []
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252 for e in err:
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253 errors.append(e[0])
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254 with open('inter.txt', 'w') as y:
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255 l = 0; a = 0
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256 for bb in bait:
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257 for lst in data:
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258 if proteins[a] not in errors:
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259 y.write(header[bait_index[l]] + '\t' + bb[1] + '\t' + proteins[a] + '\t'
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260 + lst[bait_index[l]] + '\n')
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261 a += 1
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262 if a == len(proteins):
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263 l += 1; a = 0
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264
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265
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266 def bait_check(bait, Scaffold_input):
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267 # Check that bait names share Scaffold header titles.
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268 bait_in = readtab(bait)
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269 header = read_Scaffold(Scaffold_input).header
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270 for i in bait_in:
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271 if i[0] not in header:
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272 sys.exit("Bait must share header titles with Scaffold output")
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273
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274 if __name__ == '__main__':
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275 main(infile, baitfile)
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276
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277 os.rename("inter.txt", sys.argv[4])
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278 os.rename("bait.txt", sys.argv[7])
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