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