Mercurial > repos > cpt > cpt_putative_isp

annotate generate-putative-isp.py @ 9:9fa911974de6 draft default tip

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planemo upload commit a4912b5d710e0082b764a8c90bf184078e74d83d-dirty
author cpt
date Fri, 20 Sep 2024 03:38:42 +0000
parents bc16792ecfd2
children
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1 #!/usr/bin/env python
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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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6 import argparse
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7 from cpt import OrfFinder
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8 import regex as re
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9 from spaninFuncs import *
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10
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11
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12 if __name__ == "__main__":
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13
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14 parser = argparse.ArgumentParser(
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15 description="Get putative protein candidates for spanins"
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16 )
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17 parser.add_argument(
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18 "fasta_file", type=argparse.FileType("r"), help="Fasta file"
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19 ) # the "input" argument
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20
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21 parser.add_argument(
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22 "-f",
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23 "--format",
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24 dest="seq_format",
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25 default="fasta",
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26 help="Sequence format (e.g. fasta, fastq, sff)",
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27 ) # optional formats for input, currently just going to do ntFASTA
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28
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29 parser.add_argument(
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30 "--strand",
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31 dest="strand",
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32 choices=("both", "forward", "reverse"),
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33 default="both",
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34 help="select strand",
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35 ) # Selection of +, -, or both strands
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36
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37 parser.add_argument(
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38 "--table", dest="table", default=11, help="NCBI Translation table", type=int
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39 ) # Uses "default" NCBI codon table. This should always (afaik) be what we want...
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40
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41 parser.add_argument(
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42 "-t",
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43 "--ftype",
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44 dest="ftype",
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45 choices=("CDS", "ORF"),
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46 default="ORF",
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47 help="Find ORF or CDSs",
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48 ) # "functional type(?)" --> Finds ORF or CDS, for this we want just the ORF
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49
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50 parser.add_argument(
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51 "-e",
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52 "--ends",
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53 dest="ends",
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54 choices=("open", "closed"),
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55 default="closed",
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56 help="Open or closed. Closed ensures start/stop codons are present",
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57 ) # includes the start and stop codon
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58
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59 parser.add_argument(
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60 "-m",
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61 "--mode",
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62 dest="mode",
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63 choices=("all", "top", "one"),
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64 default="all", # I think we want this to JUST be all...nearly always
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65 help="Output all ORFs/CDSs from sequence, all ORFs/CDSs with max length, or first with maximum length",
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66 )
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67
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68 parser.add_argument(
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69 "--switch",
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70 dest="switch",
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71 default="all",
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72 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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73 )
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74 # isp parameters
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75 parser.add_argument(
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76 "--isp_min_len",
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77 dest="isp_min_len",
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78 default=60,
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79 help="Minimum ORF length, measured in codons",
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80 type=int,
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81 )
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82 parser.add_argument(
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83 "--isp_on",
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84 dest="out_isp_nuc",
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85 type=argparse.FileType("w"),
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86 default="_out_isp.fna",
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87 help="Output nucleotide sequences, FASTA",
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88 )
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89 parser.add_argument(
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90 "--isp_op",
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91 dest="out_isp_prot",
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92 type=argparse.FileType("w"),
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93 default="_out_isp.fa",
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94 help="Output protein sequences, FASTA",
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95 )
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96 parser.add_argument(
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97 "--isp_ob",
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98 dest="out_isp_bed",
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99 type=argparse.FileType("w"),
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100 default="_out_isp.bed",
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101 help="Output BED file",
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102 )
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103 parser.add_argument(
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104 "--isp_og",
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105 dest="out_isp_gff3",
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106 type=argparse.FileType("w"),
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107 default="_out_isp.gff3",
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108 help="Output GFF3 file",
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109 )
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110 parser.add_argument(
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111 "--isp_min_dist",
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112 dest="isp_min_dist",
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113 default=10,
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114 help="Minimal distance to first AA of TMD, measured in AA",
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115 type=int,
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116 )
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117 parser.add_argument(
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118 "--isp_max_dist",
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119 dest="isp_max_dist",
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120 default=30,
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121 help="Maximum distance to first AA of TMD, measured in AA",
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122 type=int,
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123 )
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124 parser.add_argument(
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125 "--putative_isp",
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126 dest="putative_isp_fa",
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127 type=argparse.FileType("w"),
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128 default="_putative_isp.fa",
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129 help="Output of putative FASTA file",
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130 )
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131 parser.add_argument(
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132 "--min_tmd_size",
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133 dest="min_tmd_size",
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134 default=10,
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135 help="Minimal size of the TMD domain",
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136 type=int,
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137 )
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138 parser.add_argument(
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139 "--max_tmd_size",
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140 dest="max_tmd_size",
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141 default=20,
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142 help="Maximum size of the TMD domain",
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143 type=int,
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144 )
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145 parser.add_argument(
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146 "--summary_isp_txt",
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147 dest="summary_isp_txt",
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148 type=argparse.FileType("w"),
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149 default="_summary_isp.txt",
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150 help="Summary statistics on putative i-spanins",
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151 )
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152 parser.add_argument(
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153 "--putative_isp_gff",
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154 dest="putative_isp_gff",
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155 type=argparse.FileType("w"),
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156 default="_putative_isp.gff3",
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157 help="gff3 output for putative i-spanins",
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158 )
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159
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160 parser.add_argument(
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161 "--max_isp",
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162 dest="max_isp",
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163 default=230,
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164 help="Maximum size of the ISP",
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165 type=int,
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166 )
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167
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168 parser.add_argument("--isp_mode", action="store_true", default=True)
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169
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170 parser.add_argument(
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171 "--peri_min",
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172 type=int,
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173 default=18,
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174 help="amount of residues after TMD is found min",
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175 )
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176
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177 parser.add_argument(
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178 "--peri_max",
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179 type=int,
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180 default=206,
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181 help="amount of residues after TMD is found max",
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182 )
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183 # parser.add_argument('-v', action='version', version='0.3.0') # Is this manually updated?
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184 args = parser.parse_args()
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185 the_args = vars(parser.parse_args())
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186
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187 ### isp output, naive ORF finding:
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188 isps = OrfFinder(args.table, args.ftype, args.ends, args.isp_min_len, args.strand)
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189 isps.locate(
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190 args.fasta_file,
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191 args.out_isp_nuc,
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192 args.out_isp_prot,
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193 args.out_isp_bed,
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194 args.out_isp_gff3,
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195 )
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196 """
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197 >T7_EIS MLEFLRKLIPWVLVGMLFGLGWHLGSDSMDAKWKQEVHNEYVKRVEAAKSTQRAIGAVSAKYQEDLAALEGSTDRIISDLRSDNKRLRVRVKTTGISDGQCGFEPDGRAELDDRDAKRILAVTQKGDAWIRALQDTIRELQRK
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198 >lambda_EIS MSRVTAIISALVICIIVCLSWAVNHYRDNAITYKAQRDKNARELKLANAAITDMQMRQRDVAALDAKYTKELADAKAENDALRDDVAAGRRRLHIKAVCQSVREATTASGVDNAASPRLADTAERDYFTLRERLITMQKQLEGTQKYINEQCR
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199 """
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200 args.fasta_file.close()
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201 args.fasta_file = open(args.fasta_file.name, "r")
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202 args.out_isp_prot.close()
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203 args.out_isp_prot = open(args.out_isp_prot.name, "r")
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diff changeset
204
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205 pairs = tuple_fasta(fasta_file=args.out_isp_prot)
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206
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207 have_tmd = [] # empty candidates list to be passed through the user input criteria
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208
3
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209 for each_pair in pairs:
1
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210 if len(each_pair[1]) <= args.max_isp:
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211 try:
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212 have_tmd += find_tmd(
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213 pair=each_pair,
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214 minimum=args.isp_min_dist,
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215 maximum=args.isp_max_dist,
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216 TMDmin=args.min_tmd_size,
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217 TMDmax=args.max_tmd_size,
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218 isp_mode=args.isp_mode,
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219 peri_min=args.peri_min,
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220 peri_max=args.peri_max,
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221 )
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222 except TypeError:
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223 continue
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224
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225 if args.switch == "all":
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226 pass
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227 else:
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228 # for each_pair in have_lipo:
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229 range_of = args.switch
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230 range_of = re.search(("[\d]+:[\d]+"), range_of).group(0)
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231 start = int(range_of.split(":")[0])
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232 end = int(range_of.split(":")[1])
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233 have_tmd = parse_a_range(pair=have_tmd, start=start, end=end)
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parents:
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234
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235 total_isp = len(have_tmd)
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236
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237 # ORF = [] # mightttttttttttt use eventually
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238 length = [] # grabbing length of the sequences
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239 candidate_dict = {k: v for k, v in have_tmd}
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240 with args.putative_isp_fa as f:
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241 for desc, s in candidate_dict.items(): # description / sequence
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242 f.write(">" + str(desc))
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243 f.write("\n" + lineWrapper(str(s).replace("*", "")) + "\n")
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244 length.append(len(s))
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245 # ORF.append(desc)
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246 if not length:
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247 raise Exception("Parameters yielded no candidates.")
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248 bot_size = min(length)
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249 top_size = max(length)
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250 avg = (sum(length)) / total_isp
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251 n = len(length)
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252 if n == 0:
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253 raise Exception("no median for empty data")
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254 if n % 2 == 1:
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255 med = length[n // 2]
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256 else:
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257 i = n // 2
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258 med = (length[i - 1] + length[i]) / 2
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259
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260 #### Extra statistics
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261 args.out_isp_prot.close()
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262 all_orfs = open(args.out_isp_prot.name, "r")
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263 all_isps = open(args.putative_isp_fa.name, "r")
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264 # record = SeqIO.read(all_orfs, "fasta")
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265 # print(len(record))
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266 n = 0
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267 for line in all_orfs:
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268 if line.startswith(">"):
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269 n += 1
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270 all_orfs_counts = n
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271
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272 c = 0
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273 for line in all_isps:
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274 if line.startswith(">"):
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275 c += 1
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276 all_isps_counts = c
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277
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278 # print(f"{n} -> {c}")
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279 # count = 0
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280 # for feature in record.features:
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281 # count += 1
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282 # print(count)
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283
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284 with args.summary_isp_txt as f:
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285 f.write("total potential o-spanins: " + str(total_isp) + "\n")
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286 f.write("average length (AA): " + str(avg) + "\n")
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287 f.write("median length (AA): " + str(med) + "\n")
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288 f.write("maximum orf in size (AA): " + str(top_size) + "\n")
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289 f.write("minimum orf in size (AA): " + str(bot_size) + "\n")
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290 f.write("ratio of isps found from naive orfs: " + str(c) + "/" + str(n))
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291
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292 # Output the putative list in gff3 format
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293 args.putative_isp_fa = open(args.putative_isp_fa.name, "r")
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294 gff_data = prep_a_gff3(
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295 fa=args.putative_isp_fa, spanin_type="isp", org=args.fasta_file
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296 )
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297 write_gff3(data=gff_data, output=args.putative_isp_gff)
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298
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299 """https://docs.python.org/3.4/library/subprocess.html"""
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300 """https://github.tamu.edu/CPT/Galaxy-Tools/blob/f0bf4a4b8e5124d4f3082d21b738dfaa8e1a3cf6/tools/phage/transmembrane.py"""