Mercurial > repos > cpt > cpt_putative_isp

annotate generate-putative-isp.py @ 1:4e02e6e9e77d draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:51:35 +0000
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1
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1 #!/usr/bin/env python
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2
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3 ##### findSpanin.pl --> findSpanin.py
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4 ######### Incooperated from the findSpanin.pl script, but better and more snakey.
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5
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6 import argparse
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7 from cpt import OrfFinder
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8 from Bio import SeqIO
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9 from Bio import Seq
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10 import re
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11 from spaninFuncs import *
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12 import os
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13
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14 # if __name__ == '__main__':
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15 # pass
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16 ###############################################################################
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17
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18 if __name__ == "__main__":
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19
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20 # Common parameters for both ISP / OSP portion of script
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21
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22 parser = argparse.ArgumentParser(
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23 description="Get putative protein candidates for spanins"
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24 )
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25 parser.add_argument(
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26 "fasta_file", type=argparse.FileType("r"), help="Fasta file"
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27 ) # the "input" argument
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28
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29 parser.add_argument(
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30 "-f",
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31 "--format",
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32 dest="seq_format",
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33 default="fasta",
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34 help="Sequence format (e.g. fasta, fastq, sff)",
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35 ) # optional formats for input, currently just going to do ntFASTA
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36
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37 parser.add_argument(
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38 "--strand",
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39 dest="strand",
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40 choices=("both", "forward", "reverse"),
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41 default="both",
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42 help="select strand",
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43 ) # Selection of +, -, or both strands
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44
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45 parser.add_argument(
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46 "--table", dest="table", default=11, help="NCBI Translation table", type=int
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47 ) # Uses "default" NCBI codon table. This should always (afaik) be what we want...
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48
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49 parser.add_argument(
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50 "-t",
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51 "--ftype",
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52 dest="ftype",
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53 choices=("CDS", "ORF"),
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54 default="ORF",
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55 help="Find ORF or CDSs",
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56 ) # "functional type(?)" --> Finds ORF or CDS, for this we want just the ORF
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57
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58 parser.add_argument(
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59 "-e",
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60 "--ends",
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61 dest="ends",
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62 choices=("open", "closed"),
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63 default="closed",
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64 help="Open or closed. Closed ensures start/stop codons are present",
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65 ) # includes the start and stop codon
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66
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67 parser.add_argument(
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68 "-m",
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69 "--mode",
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70 dest="mode",
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71 choices=("all", "top", "one"),
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72 default="all", # I think we want this to JUST be all...nearly always
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73 help="Output all ORFs/CDSs from sequence, all ORFs/CDSs with max length, or first with maximum length",
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74 )
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75
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76 parser.add_argument(
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77 "--switch",
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78 dest="switch",
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79 default="all",
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80 help="switch between ALL putative osps, or a range. If not all, insert a range of two integers separated by a colon (:). Eg: 1234:4321",
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81 )
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82 # isp parameters
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83 parser.add_argument(
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84 "--isp_min_len",
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85 dest="isp_min_len",
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86 default=60,
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87 help="Minimum ORF length, measured in codons",
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88 type=int,
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89 )
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90 parser.add_argument(
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91 "--isp_on",
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92 dest="out_isp_nuc",
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93 type=argparse.FileType("w"),
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94 default="_out_isp.fna",
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95 help="Output nucleotide sequences, FASTA",
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96 )
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97 parser.add_argument(
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98 "--isp_op",
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99 dest="out_isp_prot",
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100 type=argparse.FileType("w"),
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101 default="_out_isp.fa",
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102 help="Output protein sequences, FASTA",
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103 )
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104 parser.add_argument(
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105 "--isp_ob",
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106 dest="out_isp_bed",
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107 type=argparse.FileType("w"),
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108 default="_out_isp.bed",
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109 help="Output BED file",
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110 )
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111 parser.add_argument(
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112 "--isp_og",
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113 dest="out_isp_gff3",
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114 type=argparse.FileType("w"),
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115 default="_out_isp.gff3",
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116 help="Output GFF3 file",
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117 )
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118 parser.add_argument(
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119 "--isp_min_dist",
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120 dest="isp_min_dist",
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121 default=10,
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122 help="Minimal distance to first AA of TMD, measured in AA",
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123 type=int,
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124 )
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125 parser.add_argument(
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126 "--isp_max_dist",
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127 dest="isp_max_dist",
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128 default=30,
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129 help="Maximum distance to first AA of TMD, measured in AA",
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130 type=int,
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131 )
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132 parser.add_argument(
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133 "--putative_isp",
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134 dest="putative_isp_fa",
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135 type=argparse.FileType("w"),
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136 default="_putative_isp.fa",
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137 help="Output of putative FASTA file",
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138 )
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139 parser.add_argument(
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140 "--min_tmd_size",
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141 dest="min_tmd_size",
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142 default=10,
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143 help="Minimal size of the TMD domain",
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144 type=int,
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145 )
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146 parser.add_argument(
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147 "--max_tmd_size",
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148 dest="max_tmd_size",
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149 default=20,
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150 help="Maximum size of the TMD domain",
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151 type=int,
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152 )
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153 parser.add_argument(
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154 "--summary_isp_txt",
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155 dest="summary_isp_txt",
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156 type=argparse.FileType("w"),
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157 default="_summary_isp.txt",
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158 help="Summary statistics on putative i-spanins",
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159 )
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160 parser.add_argument(
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161 "--putative_isp_gff",
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162 dest="putative_isp_gff",
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163 type=argparse.FileType("w"),
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164 default="_putative_isp.gff3",
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165 help="gff3 output for putative i-spanins",
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166 )
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167
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168 parser.add_argument(
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169 "--max_isp",
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170 dest="max_isp",
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171 default=230,
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172 help="Maximum size of the ISP",
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173 type=int,
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174 )
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175
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176 parser.add_argument("--isp_mode", action="store_true", default=True)
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177
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178 parser.add_argument(
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179 "--peri_min",
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180 type=int,
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181 default=18,
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182 help="amount of residues after TMD is found min",
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183 )
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184
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185 parser.add_argument(
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186 "--peri_max",
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187 type=int,
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188 default=206,
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189 help="amount of residues after TMD is found max",
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190 )
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191 # parser.add_argument('-v', action='version', version='0.3.0') # Is this manually updated?
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192 args = parser.parse_args()
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193 the_args = vars(parser.parse_args())
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194
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195 ### isp output, naive ORF finding:
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196 isps = OrfFinder(args.table, args.ftype, args.ends, args.isp_min_len, args.strand)
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197 isps.locate(
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198 args.fasta_file,
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199 args.out_isp_nuc,
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200 args.out_isp_prot,
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201 args.out_isp_bed,
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202 args.out_isp_gff3,
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203 )
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204 """
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205 >T7_EIS MLEFLRKLIPWVLVGMLFGLGWHLGSDSMDAKWKQEVHNEYVKRVEAAKSTQRAIGAVSAKYQEDLAALEGSTDRIISDLRSDNKRLRVRVKTTGISDGQCGFEPDGRAELDDRDAKRILAVTQKGDAWIRALQDTIRELQRK
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206 >lambda_EIS MSRVTAIISALVICIIVCLSWAVNHYRDNAITYKAQRDKNARELKLANAAITDMQMRQRDVAALDAKYTKELADAKAENDALRDDVAAGRRRLHIKAVCQSVREATTASGVDNAASPRLADTAERDYFTLRERLITMQKQLEGTQKYINEQCR
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207 """
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208 args.fasta_file.close()
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209 args.fasta_file = open(args.fasta_file.name, "r")
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210 args.out_isp_prot.close()
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211 args.out_isp_prot = open(args.out_isp_prot.name, "r")
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212
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213 pairs = tuple_fasta(fasta_file=args.out_isp_prot)
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214
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215 # print(pairs)
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216
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217 have_tmd = [] # empty candidates list to be passed through the user input criteria
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218
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219 for (
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220 each_pair
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221 ) in (
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222 pairs
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223 ): # grab transmembrane domains from spaninFuncts (queries for lysin snorkels # and a range of hydrophobic regions that could be TMDs)
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224 if len(each_pair[1]) <= args.max_isp:
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225 try:
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226 have_tmd += find_tmd(
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227 pair=each_pair,
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228 minimum=args.isp_min_dist,
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229 maximum=args.isp_max_dist,
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230 TMDmin=args.min_tmd_size,
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231 TMDmax=args.max_tmd_size,
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232 isp_mode=args.isp_mode,
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233 peri_min=args.peri_min,
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234 peri_max=args.peri_max,
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235 )
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236 except TypeError:
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237 continue
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238
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239 if args.switch == "all":
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240 pass
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241 else:
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242 # for each_pair in have_lipo:
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243 range_of = args.switch
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244 range_of = re.search(("[\d]+:[\d]+"), range_of).group(0)
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245 start = int(range_of.split(":")[0])
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246 end = int(range_of.split(":")[1])
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247 have_tmd = parse_a_range(pair=have_tmd, start=start, end=end)
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248
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249 total_isp = len(have_tmd)
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250
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251 # ORF = [] # mightttttttttttt use eventually
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252 length = [] # grabbing length of the sequences
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253 candidate_dict = {k: v for k, v in have_tmd}
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254 with args.putative_isp_fa as f:
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255 for desc, s in candidate_dict.items(): # description / sequence
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256 f.write(">" + str(desc))
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257 f.write("\n" + lineWrapper(str(s).replace("*", "")) + "\n")
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258 length.append(len(s))
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259 # ORF.append(desc)
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260 if not length:
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261 raise Exception("Parameters yielded no candidates.")
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262 bot_size = min(length)
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263 top_size = max(length)
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264 avg = (sum(length)) / total_isp
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265 n = len(length)
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266 if n == 0:
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267 raise Exception("no median for empty data")
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268 if n % 2 == 1:
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269 med = length[n // 2]
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270 else:
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271 i = n // 2
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272 med = (length[i - 1] + length[i]) / 2
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273
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274 #### Extra statistics
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275 args.out_isp_prot.close()
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276 all_orfs = open(args.out_isp_prot.name, "r")
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277 all_isps = open(args.putative_isp_fa.name, "r")
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278 # record = SeqIO.read(all_orfs, "fasta")
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279 # print(len(record))
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280 n = 0
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281 for line in all_orfs:
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282 if line.startswith(">"):
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283 n += 1
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284 all_orfs_counts = n
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285
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286 c = 0
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287 for line in all_isps:
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288 if line.startswith(">"):
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289 c += 1
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290 all_isps_counts = c
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291
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292 # print(f"{n} -> {c}")
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293 # count = 0
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294 # for feature in record.features:
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295 # count += 1
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296 # print(count)
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297
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298 with args.summary_isp_txt as f:
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299 f.write("total potential o-spanins: " + str(total_isp) + "\n")
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300 f.write("average length (AA): " + str(avg) + "\n")
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301 f.write("median length (AA): " + str(med) + "\n")
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302 f.write("maximum orf in size (AA): " + str(top_size) + "\n")
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303 f.write("minimum orf in size (AA): " + str(bot_size) + "\n")
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304 f.write("ratio of isps found from naive orfs: " + str(c) + "/" + str(n))
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305
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306 # Output the putative list in gff3 format
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307 args.putative_isp_fa = open(args.putative_isp_fa.name, "r")
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308 gff_data = prep_a_gff3(
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309 fa=args.putative_isp_fa, spanin_type="isp", org=args.fasta_file
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310 )
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311 write_gff3(data=gff_data, output=args.putative_isp_gff)
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312
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313 """https://docs.python.org/3.4/library/subprocess.html"""
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314 """https://github.tamu.edu/CPT/Galaxy-Tools/blob/f0bf4a4b8e5124d4f3082d21b738dfaa8e1a3cf6/tools/phage/transmembrane.py"""