Mercurial > repos > bvalot > in_sillico_pcr

annotate qpcr_search.py @ 0:1f4836da4a14 draft default tip

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planemo upload for repository https://github.com/bvalot/galaxy commit d57c24d4b2c0c741d572af9ca0d09f8b82689640
author bvalot
date Tue, 14 Jun 2022 08:52:22 +0000
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1f4836da4a14 planemo upload for repository https://github.com/bvalot/galaxy commit d57c24d4b2c0c741d572af9ca0d09f8b82689640
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1 #!/usr/bin/env python3
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2 # -*- coding: utf-8 -*-
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3
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4 """Search primers/probe on database and return result"""
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5
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6 import argparse
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7 import os
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8 import subprocess
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9 import sys
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10 import tempfile
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11
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12 from Bio import SeqIO
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13
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14 gasst_exe = "Gassst"
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15 nucleo = {
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16 "R": ("A", "G"),
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17 "Y": ("C", "T"),
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18 "S": ("G", "C"),
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19 "W": ("A", "T"),
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20 "K": ("G", "T"),
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21 "M": ("A", "C"),
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22 "B": ("C", "G", "T"),
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23 "D": ("A", "G", "T"),
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24 "H": ("A", "C", "T"),
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25 "V": ("A", "C", "G"),
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26 "N": ("A", "T", "C", "G"),
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27 }
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28
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29 desc = "Search primer/probe on database and return position and errors."
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30 command = argparse.ArgumentParser(
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31 prog="primer_search.py",
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32 description=desc,
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33 usage="%(prog)s [options] forward probe reverse database",
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34 )
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35 command.add_argument(
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36 "-o",
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37 "--out",
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38 nargs="?",
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39 type=argparse.FileType("w"),
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40 default=sys.stdout,
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41 help="Return amplicon position on file, default=stdout",
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42 )
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43 command.add_argument(
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44 "-d",
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45 "--debug",
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46 nargs="?",
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47 type=argparse.FileType("w"),
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48 default=None,
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49 help="Conserve a copy of primer search, default No",
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50 )
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51 command.add_argument(
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52 "-e",
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53 "--error",
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54 nargs="?",
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55 type=int,
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56 default=1,
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57 help="Maximun error allowed on match, default=1",
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58 )
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59 command.add_argument(
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60 "-m",
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61 "--min",
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62 nargs="?",
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63 type=int,
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64 default=50,
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65 help="Min len amplicon size, default=50",
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66 )
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67 command.add_argument(
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68 "-M",
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69 "--max",
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70 nargs="?",
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71 type=int,
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72 default=200,
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73 help="Max len amplicon size, default=200",
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74 )
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75 command.add_argument(
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76 "-t", "--taxo", action="store_true", help="Parse description to report species only"
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77 )
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78 command.add_argument("forward", type=str, help="Forward primer sequence")
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79 command.add_argument("probe", type=str, help="Probe sequence")
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80 command.add_argument("reverse", type=str, help="Reverse primer sequence")
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81 command.add_argument(
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82 "database", type=argparse.FileType("r"), help="Database to search on fasta"
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83 )
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84 command.add_argument("-v", "--version", action="version", version="%(prog)s 0.3.0")
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85
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86
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87 class GassstResult:
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88 """A simple Gassst class containing result
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89 rev : True indicate if reverse primers, else forward
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90 """
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91
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92 def __init__(self, line):
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93 h = line.strip().split()
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94 if len(h) != 9:
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95 raise Exception("Line seems not correspond to gassst result\n" + line)
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96 self.primer = h[0]
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97 # self.rev = h[0] != "Forward"
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98 self.match = h[1]
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99 self.strand = int(h[2])
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100 self.start = int(h[3])
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101 self.error = int(h[5])
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102 self.stop = self.start + len(h[7])
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103
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104 def __repr__(self):
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105 return (
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106 self.match
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107 + " : "
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108 + str(self.start)
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109 + " in strand:"
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110 + str(self.strand)
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111 + " in primer: "
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112 + self.primer
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113 + " with error: "
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114 + str(self.error)
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115 )
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116
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117 def __eq__(self, other):
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118 return (
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119 isinstance(other, GassstResult)
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120 and self.primer == other.primer
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121 and self.match == other.match
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122 and self.strand == other.strand
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123 and self.start == other.start
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124 )
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125
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126 def __ne__(self, other):
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127 return not self == other
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128
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129 def __lt__(self, other):
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130 if self != other:
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131 raise Exception("Only compare equal GassstResult")
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132 return self.error < other.error
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133
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134
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135 class Amplicon:
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136 """A simple Amplicon class containing forward and reverse gassst result
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137 Add probe including
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138 """
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139
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140 def __init__(self, forw, reve):
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141 if forw.strand == reve.strand:
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142 raise Exception(
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143 "Amplicon could be in inverse strand for reverse/forward primer\n"
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144 + forw
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145 + reve
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146 )
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147 self.forw = forw
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148 self.prob = None
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149 self.reve = reve
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150 self.strand = forw.strand
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151
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152 def contain_probe(self, probe):
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153 if (
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154 min(probe.start, probe.stop) > self.get_start()
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155 and max(probe.start, probe.stop) < self.get_stop()
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156 ):
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157 self.prob = probe
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158 return True
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159 return False
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160
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161 def get_start(self):
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162 if self.strand == 0:
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163 return self.forw.start
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164 return self.reve.start
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165
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166 def get_stop(self):
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167 if self.strand == 1:
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168 return self.forw.stop
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169 return self.reve.stop
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170
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171 def get_tab_data(self):
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172 return map(
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173 str,
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174 [
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175 self.get_start(),
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176 self.get_stop(),
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177 self.forw.error,
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178 self.prob.error,
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179 self.reve.error,
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180 ],
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181 )
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182
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183 def __len__(self):
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184 return self.get_stop() - self.get_start()
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185
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186 def __repr__(self):
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187 if self.prob is None:
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188 return (
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189 str(self.get_start())
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190 + " : "
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191 + str(self.get_stop())
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192 + " in strand:"
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193 + str(self.strand)
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194 + "; error F:"
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195 + str(self.forw.error)
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196 + ",R:"
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197 + str(self.reve.error)
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198 )
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199 return (
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200 str(self.get_start())
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201 + " : "
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202 + str(self.get_stop())
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203 + " in strand:"
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204 + str(self.strand)
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205 + "; error F:"
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206 + str(self.forw.error)
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207 + ",P:"
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208 + str(self.prob.error)
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209 + ",R:"
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210 + str(self.reve.error)
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211 )
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212
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213
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214 def degenerate_primer(seq):
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215 """Iterate all possible sequence
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216 from degenerate primer
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217 """
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218 notdegene = True
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219 for i, n in enumerate(seq.upper()):
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220 if n in nucleo:
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221 notdegene = False
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222 for mod in nucleo.get(n):
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223 seq_cut = list(seq)
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224 seq_cut[i] = mod
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225 for seq2 in degenerate_primer("".join(seq_cut)):
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226 yield (seq2)
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227 break
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228 if notdegene:
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229 yield (seq)
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230
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231
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232 def write_primer_fasta(forward_de, probe_de, reverse_de):
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233 primer_fasta = tempfile.NamedTemporaryFile(delete=False, mode="w+t")
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234 for forward in degenerate_primer(forward_de):
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235 primer_fasta.write(">Forward\n" + forward + "\n")
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236 for probe in degenerate_primer(probe_de):
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237 primer_fasta.write(">Probe\n" + probe + "\n")
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238 for reverse in degenerate_primer(reverse_de):
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239 primer_fasta.write(">Reverse\n" + reverse + "\n")
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240 primer_fasta.close()
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241 return primer_fasta.name
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242
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243
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244 def performed_gassst(command):
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245 proc = subprocess.Popen(command, stderr=subprocess.PIPE, stdout=sys.stderr)
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246 error = ""
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247 for line in iter(proc.stderr.readline, b""):
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248 error += line.decode()
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249 if error != "":
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250 sys.stdout.write("Error during processing Gassst\n")
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251 raise Exception(error)
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252
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253
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254 def read_result(f_res, f_debug):
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255 result = {}
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256 for line in iter(f_res.readline, ""):
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257 if line[0] == "F" or line[0] == "R" or line[0] == "P":
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258 if f_debug is not None:
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259 f_debug.write(line)
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260 res = GassstResult(line)
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261 other_res = result.setdefault(res.match, {}).setdefault(res.primer, [])
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262 notfound = True
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263 for i, res2 in enumerate(other_res):
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264 if res == res2:
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265 notfound = False
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266 if res < res2:
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267 other_res[i] = res
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268 # print res
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269 break
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270 if notfound:
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271 other_res.append(res)
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272 return result
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273
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274
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275 def get_amplicons(result):
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276 """Function to get amplicon on a sequence from forward / reverse result"""
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277 for forw in result["Forward"]:
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278 for reve in result["Reverse"]:
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279 if forw.strand != reve.strand:
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280 amp = Amplicon(forw, reve)
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281 if amp.get_start() < amp.get_stop(): # must be side by side
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282 for probe in result["Probe"]:
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283 if amp.contain_probe(probe):
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284 yield amp
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285 break
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286 del amp
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287 else:
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288 del amp
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289
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290
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291 if __name__ == "__main__":
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292 """Performed job on execution script"""
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293 args = command.parse_args()
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294 primer_fasta = write_primer_fasta(args.forward, args.probe, args.reverse)
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parents:
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295 output_result = tempfile.NamedTemporaryFile(delete=False, mode="w+")
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296 identity = int(
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297 100 - args.error / float(max(len(args.forward), len(args.reverse))) * 100
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298 )
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299
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300 command = [
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301 gasst_exe,
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302 "-p",
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303 str(identity),
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304 "-g",
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305 "0",
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306 "-w",
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307 "6",
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308 "-h",
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309 "0",
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310 "-i",
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311 primer_fasta,
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312 "-d",
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313 args.database.name,
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314 "-o",
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315 output_result.name,
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316 ]
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317 performed_gassst(command)
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318 result = read_result(output_result, args.debug)
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319
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320 # load amplicons
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321 sys.stderr.write("Search amplicons : ")
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322 amplicons = {}
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323 for seq in result.keys():
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324 if len(result[seq]) == 3:
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325 # print "Search amplicon on seq: " + seq
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326 for amplicon in get_amplicons(result[seq]):
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327 if len(amplicon) > args.min and len(amplicon) < args.max:
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328 amplicons.setdefault(seq, []).append(amplicon)
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329 else:
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330 del amplicon
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331 # print "Find amplicons : " + str(len(amplicons[seq]))
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332 sys.stderr.write(str(sum(map(len, amplicons.values()))) + "\n\n")
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333
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334 # print amplicons
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335
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336 sys.stderr.write("Write result : ")
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337 sep = "\t"
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338 args.out.write(
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339 "Id\tAmpli number\tDescription\tStart\tStop\tError forward\tError probe\tError reverse\n"
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340 )
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341 for record in SeqIO.parse(args.database, "fasta"):
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342 if record.id not in amplicons:
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343 continue
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344 for i, amplicon in enumerate(amplicons.get(record.id)):
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345 desc = record.description.lstrip(record.id)
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346 if args.taxo:
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347 desc = record.description.split(";")[-1].strip()
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348 args.out.write(
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349 record.id
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350 + sep
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351 + str(i + 1)
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352 + sep
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353 + desc
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354 + sep
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355 + sep.join(amplicon.get_tab_data())
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356 + "\n"
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357 )
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358 sys.stderr.write("OK\n")
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359 # delete tempfile
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360 os.unlink(primer_fasta)
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361 os.unlink(output_result.name)