Mercurial > repos > cpt > cpt_putative_usp

annotate generate-putative-usp.py @ 1:f7afd1480d0f draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:51:59 +0000
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1
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1 import argparse
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2 from cpt import OrfFinder
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3 from Bio import SeqIO
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4 from Bio import Seq
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5 from CPT_GFFParser import gffParse, gffWrite
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6 from spaninFuncs import *
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7 import re
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8 import os
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9 import sys
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10
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11 """
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12 ## Note
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13 NOTE : This was made after I made the i-spanin and o-spanin tools, so there might be some methods that are used differently
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14 and overall some 'differently' written code...
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15 """
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16
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17 if __name__ == "__main__":
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18 parser = argparse.ArgumentParser(
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19 description="Get putative protein candidates for u-spanins"
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20 )
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21
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22 parser.add_argument(
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23 "fasta_file", type=argparse.FileType("r"), help="Fasta file"
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24 ) # the "input" argument
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25
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26 parser.add_argument(
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27 "--strand",
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28 dest="strand",
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29 choices=("both", "forward", "reverse"),
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30 default="both",
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31 help="select strand",
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32 ) # Selection of +, -, or both strands
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33
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34 parser.add_argument(
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35 "--table", dest="table", default=11, help="NCBI Translation table", type=int
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36 ) # Uses "default" NCBI codon table. This should always (afaik) be what we want...
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37
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38 parser.add_argument(
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39 "-t",
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40 "--ftype",
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41 dest="ftype",
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42 choices=("CDS", "ORF"),
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43 default="ORF",
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44 help="Find ORF or CDSs",
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45 ) # "functional type(?)" --> Finds ORF or CDS, for this we want just the ORF
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46
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47 parser.add_argument(
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48 "-e",
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49 "--ends",
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50 dest="ends",
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51 choices=("open", "closed"),
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52 default="closed",
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53 help="Open or closed. Closed ensures start/stop codons are present",
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54 ) # includes the start and stop codon
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55
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56 parser.add_argument(
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57 "-m",
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58 "--mode",
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59 dest="mode",
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60 choices=("all", "top", "one"),
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61 default="all", # I think we want this to JUST be all...nearly always
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62 help="Output all ORFs/CDSs from sequence, all ORFs/CDSs with max length, or first with maximum length",
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63 )
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64
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65 parser.add_argument(
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66 "--switch",
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67 dest="switch",
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68 default="all",
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69 help="switch between ALL putative usps, or a range. If not all, insert a range of two integers separated by a colon (:). Eg: 1234:4321",
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70 )
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71
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72 parser.add_argument(
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73 "--usp_on",
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74 dest="out_usp_nuc",
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75 type=argparse.FileType("w"),
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76 default="_out_usp.fna",
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77 help="Output nucleotide sequences, FASTA",
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78 )
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79 parser.add_argument(
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80 "--usp_op",
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81 dest="out_usp_prot",
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82 type=argparse.FileType("w"),
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83 default="_out_usp.fa",
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84 help="Output protein sequences, FASTA",
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85 )
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86 parser.add_argument(
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87 "--usp_ob",
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88 dest="out_usp_bed",
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89 type=argparse.FileType("w"),
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90 default="_out_usp.bed",
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91 help="Output BED file",
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92 )
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93 parser.add_argument(
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94 "--usp_og",
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95 dest="out_usp_gff3",
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96 type=argparse.FileType("w"),
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97 default="_out_usp.gff3",
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98 help="Output GFF3 file",
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99 )
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100 parser.add_argument(
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101 "--putative_usp",
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102 dest="putative_usp_fa",
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103 type=argparse.FileType("w"),
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104 default="_putative_usp.fa",
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105 help="Output of putative FASTA file",
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106 )
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107 parser.add_argument(
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108 "--summary_usp_txt",
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109 dest="summary_usp_txt",
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110 type=argparse.FileType("w"),
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111 default="_summary_usp.txt",
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112 help="Summary statistics on putative o-spanins",
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113 )
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114 parser.add_argument(
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115 "--putative_usp_gff",
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116 dest="putative_usp_gff",
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117 type=argparse.FileType("w"),
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118 default="_putative_usp.gff3",
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119 help="gff3 output for putative o-spanins",
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120 )
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121
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122 parser.add_argument(
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123 "--min_size", type=int, default=100, help="minimum size of peptide"
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124 )
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125 parser.add_argument(
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126 "--max_size", type=int, default=200, help="maximum size of peptide"
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127 )
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128 parser.add_argument(
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129 "--lipo_min_start", type=int, default=10, help="minimum start site of lipobox"
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130 )
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131 parser.add_argument(
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132 "--lipo_max_start", type=int, default=30, help="maximum end site of lipobox"
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133 )
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134 parser.add_argument(
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135 "--min_lipo_after",
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136 type=int,
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137 default=60,
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138 help="minumum amount of residues after lipobox",
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139 )
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140 parser.add_argument(
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141 "--max_lipo_after",
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142 type=int,
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143 default=160,
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144 help="maximum amount of residues after lipobox",
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145 )
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146 parser.add_argument(
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147 "--tmd_min_start", type=int, default=75, help="minumum start site of TMD"
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148 )
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149 parser.add_argument(
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150 "--tmd_max_start", type=int, default=200, help="maximum end site of TMD"
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151 )
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152 parser.add_argument(
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153 "--tmd_min_size", type=int, default=15, help="minimum size of TMD"
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154 )
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155 parser.add_argument(
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156 "--tmd_max_size", type=int, default=25, help="maximum size of TMD"
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157 )
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158
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159 args = parser.parse_args()
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160
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161 the_args = vars(parser.parse_args())
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162
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163 ### usp output, naive ORF finding:
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164 usps = OrfFinder(args.table, args.ftype, args.ends, args.min_size, args.strand)
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165 usps.locate(
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166 args.fasta_file,
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167 args.out_usp_nuc,
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168 args.out_usp_prot,
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169 args.out_usp_bed,
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170 args.out_usp_gff3,
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171 )
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172
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173 args.fasta_file.close()
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174 args.fasta_file = open(args.fasta_file.name, "r")
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175 args.out_usp_prot.close()
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176 args.out_usp_prot = open(args.out_usp_prot.name, "r")
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177
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178 pairs = tuple_fasta(fasta_file=args.out_usp_prot)
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179 have_lipo = []
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180
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181 for each_pair in pairs:
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182 if len(each_pair[1]) <= args.max_size:
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183 try:
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184 have_lipo += find_lipobox(
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185 pair=each_pair,
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186 minimum=args.lipo_min_start,
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187 maximum=args.lipo_max_start,
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188 min_after=args.min_lipo_after,
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189 max_after=args.max_lipo_after,
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190 )
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191 except (IndexError, TypeError):
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192 continue
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193
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194 # print(len(have_lipo))
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195 # print(have_lipo)
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196
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197 have_tmd_and_lipo = []
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198 # print(args.tmd_min_start)
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199 # print(args.tmd_max_start)
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200 # print(args.tmd_min_size)
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201 # print(args.tmd_max_size)
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202
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203 for each_pair in have_lipo:
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204 try:
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205 have_tmd_and_lipo += find_tmd(
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206 pair=each_pair,
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207 minimum=args.tmd_min_start,
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208 maximum=args.tmd_max_start,
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209 TMDmin=args.tmd_min_size,
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210 TMDmax=args.tmd_max_size,
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211 )
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212 except (IndexError, TypeError):
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213 continue
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214
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215 # print(len(have_tmd_and_lipo))
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216 # print(have_tmd_and_lipo)
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217
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218 if args.switch == "all":
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219 pass
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220 else:
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221 range_of = args.switch
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222 range_of = re.search(("[\d]+:[\d]+"), range_of).group(0)
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223 start = int(range_of.split(":")[0])
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224 end = int(range_of.split(":")[1])
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225 have_lipo = parse_a_range(pair=have_tmd_and_lipo, start=start, end=end)
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226
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227 total_have_tmd_and_lipo = len(have_tmd_and_lipo)
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228
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229 ORF = []
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230 length = []
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231 candidate_dict = {k: v for k, v in have_tmd_and_lipo}
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232 with args.putative_usp_fa as f:
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233 for desc, s in candidate_dict.items():
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234 f.write(">" + str(desc))
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235 f.write("\n" + lineWrapper(str(s).replace("*", "")) + "\n")
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236 length.append(len(s))
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237 ORF.append(desc)
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238 #### Extra statistics
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239 args.out_usp_prot.close()
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240 all_orfs = open(args.out_usp_prot.name, "r")
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241 all_isps = open(args.putative_usp_fa.name, "r")
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242 # record = SeqIO.read(all_orfs, "fasta")
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243 # print(len(record))
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244 n = 0
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245 for line in all_orfs:
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246 if line.startswith(">"):
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247 n += 1
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248 all_orfs_counts = n
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249
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250 c = 0
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251 for line in all_isps:
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252 if line.startswith(">"):
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253 c += 1
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254 all_isps_counts = c
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255
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256 if ORF:
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257 bot_size = min(length)
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258 top_size = max(length)
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259 avg = (sum(length)) / total_have_tmd_and_lipo
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260 n = len(length)
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261 if n == 0:
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262 raise Exception("no median for empty data")
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263 if n % 2 == 1:
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264 med = length[n // 2]
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265 else:
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266 i = n // 2
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267 med = (length[i - 1] + length[i]) / 2
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268 with args.summary_usp_txt as f:
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269 f.write("total potential u-spanins: " + str(total_have_tmd_and_lipo) + "\n")
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270 f.write("average length (AA): " + str(avg) + "\n")
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271 f.write("median length (AA): " + str(med) + "\n")
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272 f.write("maximum orf in size (AA): " + str(top_size) + "\n")
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273 f.write("minimum orf in size (AA): " + str(bot_size) + "\n")
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274 f.write("ratio of isps found from naive orfs: " + str(c) + "/" + str(n))
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275
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276 args.putative_usp_fa = open(args.putative_usp_fa.name, "r")
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277 gff_data = prep_a_gff3(
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278 fa=args.putative_usp_fa, spanin_type="usp", org=args.fasta_file
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279 )
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280 write_gff3(data=gff_data, output=args.putative_usp_gff)
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281 else:
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282 with args.summary_usp_txt as f:
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283 f.write("No Candidate USPs found")
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284 if have_lipo:
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285 f.write("\nLipoboxes were found here:\n")
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286 for each_lipo in have_lipo:
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287 f.write(">" + str(each_lipo[0]))
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288 f.write("\n" + lineWrapper(each_lipo[1].replace("*", "")) + "\n")
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289 else:
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290 f.write("\nNo Lipobox(es) were found within search restraints")