Mercurial > repos > cpt > cpt_putative_isp

annotate spaninFuncs.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 4e02e6e9e77d
children
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1
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1 """
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2 PREMISE
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3 ### Functions/Classes that are used in both generate-putative-osp.py and generate-putative-isp.py
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4 ###### Main premise here is to make the above scripts a little more DRY, as well as easily readable for execution.
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5 ###### Documentation will ATTEMPT to be thourough here
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6 """
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7
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8 import re
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9 from Bio import SeqIO
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10 from Bio import Seq
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11 from collections import OrderedDict
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12
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13 # Not written in OOP for a LITTLE bit of trying to keep the complication down in case adjustments are needed by someone else.
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14 # Much of the manipulation is string based; so it should be straightforward as well as moderately quick
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15 ################## GLobal Variables
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16 Lys = "K"
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17
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18
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19 def check_back_end_snorkels(seq, tmsize):
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20 """
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21 Searches through the backend of a potential TMD snorkel. This is the 2nd part of a TMD snorkel lysine match.
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22 --> seq : should be the sequence fed from the "search_region" portion of the sequence
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23 --> tmsize : size of the potential TMD being investigated
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24 """
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25 found = []
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26 if seq[tmsize - 4] == Lys and re.search(("[FIWLVMYCATGS]"), seq[tmsize - 5]):
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27 found = "match"
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28 return found
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29 elif seq[tmsize - 3] == Lys and re.search(("[FIWLVMYCATGS]"), seq[tmsize - 4]):
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30 found = "match"
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31 return found
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32 elif seq[tmsize - 2] == Lys and re.search(("[FIWLVMYCATGS]"), seq[tmsize - 3]):
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33 found = "match"
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34 return found
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35 elif seq[tmsize - 1] == Lys and re.search(("[FIWLVMYCATGS]"), seq[tmsize - 2]):
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36 found = "match"
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37 return found
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38 else:
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39 found = "NOTmatch"
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40 return found
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41
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42
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43 def prep_a_gff3(fa, spanin_type, org):
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44 """
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45 Function parses an input detailed 'fa' file and outputs a 'gff3' file
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46 ---> fa = input .fa file
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47 ---> output = output a returned list of data, easily portable to a gff3 next
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48 ---> spanin_type = 'isp' or 'osp'
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49 """
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50 with org as f:
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51 header = f.readline()
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52 orgacc = header.split(" ")
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53 orgacc = orgacc[0].split(">")[1].strip()
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54 fa_zip = tuple_fasta(fa)
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55 data = []
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56 for a_pair in fa_zip:
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57 # print(a_pair)
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58 if re.search(("(\[1\])"), a_pair[0]):
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59 strand = "+"
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60 elif re.search(("(\[-1\])"), a_pair[0]):
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61 strand = "-" # column 7
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62 start = re.search(("[\d]+\.\."), a_pair[0]).group(0).split("..")[0] # column 4
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63 end = re.search(("\.\.[\d]+"), a_pair[0]).group(0).split("..")[1] # column 5
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64 orfid = re.search(("(ORF)[\d]+"), a_pair[0]).group(0) # column 1
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65 if spanin_type == "isp":
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66 methodtype = "CDS" # column 3
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67 spanin = "isp"
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68 elif spanin_type == "osp":
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69 methodtype = "CDS" # column 3
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70 spanin = "osp"
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71 elif spanin_type == "usp":
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72 methodtype = "CDS"
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73 spanin = "usp"
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74 else:
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75 raise "need to input spanin type"
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76 source = "cpt.py|putative-*.py" # column 2
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77 score = "." # column 6
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78 phase = "." # column 8
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79 attributes = (
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80 "ID=" + orgacc + "|" + orfid + ";ALIAS=" + spanin + ";SEQ=" + a_pair[1]
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81 ) # column 9
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82 sequence = [
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83 [orgacc, source, methodtype, start, end, score, strand, phase, attributes]
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84 ]
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85 data += sequence
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86 return data
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87
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88
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89 def write_gff3(data, output="results.gff3"):
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90 """
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91 Parses results from prep_a_gff3 into a gff3 file
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92 ---> input : list from prep_a_gff3
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93 ---> output : gff3 file
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94 """
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95 data = data
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96 filename = output
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97 with filename as f:
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98 f.write("#gff-version 3\n")
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99 for value in data:
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100 f.write(
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101 "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(
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102 value[0],
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103 value[1],
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104 value[2],
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105 value[3],
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106 value[4],
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107 value[5],
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108 value[6],
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109 value[7],
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110 value[8],
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111 )
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112 )
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113 f.close()
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114
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115
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116 def find_tmd(
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117 pair,
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118 minimum=10,
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119 maximum=30,
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120 TMDmin=10,
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121 TMDmax=20,
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122 isp_mode=False,
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123 peri_min=18,
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124 peri_max=206,
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125 ):
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126 """
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127 Function that searches for lysine snorkels and then for a spanning hydrophobic region that indicates a potential TMD
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128 ---> pair : Input of tuple with description and AA sequence (str)
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129 ---> minimum : How close from the initial start codon a TMD can be within
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130 ---> maximum : How far from the initial start codon a TMD can be within
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131 ---> TMDmin : The minimum size that a transmembrane can be (default = 10)
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132 ---> TMDmax : The maximum size tha ta transmembrane can be (default = 20)
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133 """
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134 # hydrophobicAAs = ['P', 'F', 'I', 'W', 'L', 'V', 'M', 'Y', 'C', 'A', 'T', 'G', 'S']
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135 tmd = []
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136 s = str(pair[1]) # sequence being analyzed
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137 # print(s) # for trouble shooting
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138 if maximum > len(s):
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139 maximum = len(s)
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140 search_region = s[minimum - 1 : maximum + 1]
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141 # print(f"this is the search region: {search_region}")
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142 # print(search_region) # for trouble shooting
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143
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144 for tmsize in range(TMDmin, TMDmax + 1, 1):
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145 # print(f"this is the current tmsize we're trying: {tmsize}")
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146 # print('==============='+str(tmsize)+'================') # print for troubleshooting
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147 pattern = (
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148 "[PFIWLVMYCATGS]{" + str(tmsize) + "}"
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149 ) # searches for these hydrophobic residues tmsize total times
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150 # print(pattern)
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151 # print(f"sending to regex: {search_region}")
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152 if re.search(
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153 ("[K]"), search_region[1:8]
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154 ): # grabbing one below with search region, so I want to grab one ahead here when I query.
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155 store_search = re.search(
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156 ("[K]"), search_region[1:8]
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157 ) # storing regex object
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158 where_we_are = store_search.start() # finding where we got the hit
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159 if re.search(
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160 ("[PFIWLVMYCATGS]"), search_region[where_we_are + 1]
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161 ) and re.search(
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162 ("[PFIWLVMYCATGS]"), search_region[where_we_are - 1]
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163 ): # hydrophobic neighbor
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164 # try:
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165 g = re.search(
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166 ("[PFIWLVMYCATGS]"), search_region[where_we_are + 1]
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167 ).group()
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168 backend = check_back_end_snorkels(search_region, tmsize)
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169 if backend == "match":
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170 if isp_mode:
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171 g = re.search((pattern), search_region).group()
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172 end_of_tmd = re.search((g), s).end() + 1
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173 amt_peri = len(s) - end_of_tmd
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174 if peri_min <= amt_peri <= peri_max:
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175 pair_desc = pair[0] + ", peri_count~=" + str(amt_peri)
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176 new_pair = (pair_desc, pair[1])
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177 tmd.append(new_pair)
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178 else:
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179 tmd.append(pair)
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180 else:
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181 continue
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182 # else:
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183 # print("I'm continuing out of snorkel loop")
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184 # print(f"{search_region}")
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185 # continue
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186 if re.search((pattern), search_region):
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187 # print(f"found match: {}")
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188 # print("I AM HEREEEEEEEEEEEEEEEEEEEEEEE")
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189 # try:
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190 if isp_mode:
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191 g = re.search((pattern), search_region).group()
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192 end_of_tmd = re.search((g), s).end() + 1
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193 amt_peri = len(s) - end_of_tmd
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194 if peri_min <= amt_peri <= peri_max:
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195 pair_desc = pair[0] + ", peri_count~=" + str(amt_peri)
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196 new_pair = (pair_desc, pair[1])
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197 tmd.append(new_pair)
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198 else:
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199 tmd.append(pair)
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200 else:
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201 continue
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202
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203 return tmd
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204
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205
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206 def find_lipobox(
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207 pair, minimum=10, maximum=50, min_after=30, max_after=185, regex=1, osp_mode=False
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208 ):
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209 """
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210 Function that takes an input tuple, and will return pairs of sequences to their description that have a lipoobox
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211 ---> minimum - min distance from start codon to first AA of lipobox
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212 ---> maximum - max distance from start codon to first AA of lipobox
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213 ---> regex - option 1 (default) => more strict regular expression ; option 2 => looser selection, imported from LipoRy
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214
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215 """
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216 if regex == 1:
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217 pattern = "[ILMFTV][^REKD][GAS]C" # regex for Lipobox from findSpanin.pl
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218 elif regex == 2:
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219 pattern = "[ACGSILMFTV][^REKD][GAS]C" # regex for Lipobox from LipoRy
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220
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221 candidates = []
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222 s = str(pair[1])
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223 # print(s) # trouble shooting
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224 search_region = s[
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225 minimum - 1 : maximum + 5
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226 ] # properly slice the input... add 4 to catch if it hangs off at max input
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227 # print(search_region) # trouble shooting
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228 patterns = ["[ILMFTV][^REKD][GAS]C", "AW[AGS]C"]
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229 for pattern in patterns:
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230 # print(pattern) # trouble shooting
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231 if re.search((pattern), search_region): # lipobox must be WITHIN the range...
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232 # searches the sequence with the input RegEx AND omits if
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233 g = re.search(
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234 (pattern), search_region
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235 ).group() # find the exact group match
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236 amt_peri = len(s) - re.search((g), s).end() + 1
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237 if min_after <= amt_peri <= max_after: # find the lipobox end region
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238 if osp_mode:
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239 pair_desc = pair[0] + ", peri_count~=" + str(amt_peri)
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240 new_pair = (pair_desc, pair[1])
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241 candidates.append(new_pair)
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242 else:
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243 candidates.append(pair)
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244
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245 return candidates
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246
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247
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248 def tuple_fasta(fasta_file):
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249 """
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250 #### INPUT: Fasta File
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251 #### OUTPUT: zipped (zip) : pairwise relationship of description to sequence
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252 ####
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253 """
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254 fasta = SeqIO.parse(fasta_file, "fasta")
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255 descriptions = []
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256 sequences = []
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257 for r in fasta: # iterates and stores each description and sequence
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258 description = r.description
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259 sequence = str(r.seq)
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260 if (
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261 sequence[0] != "I"
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262 ): # the translation table currently has I as a potential start codon ==> this will remove all ORFs that start with I
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263 descriptions.append(description)
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264 sequences.append(sequence)
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265 else:
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266 continue
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267
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268 return zip(descriptions, sequences)
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269
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270
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271 def lineWrapper(text, charactersize=60):
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272
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273 if len(text) <= charactersize:
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274 return text
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275 else:
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276 return (
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277 text[:charactersize]
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278 + "\n"
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279 + lineWrapper(text[charactersize:], charactersize)
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280 )
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281
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282
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283 def getDescriptions(fasta):
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284 """
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285 Takes an output FASTA file, and parses retrieves the description headers. These headers contain information needed
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286 for finding locations of a potential i-spanin and o-spanin proximity to one another.
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287 """
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288 desc = []
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289 with fasta as f:
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290 for line in f:
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291 if line.startswith(">"):
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292 desc.append(line)
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293 return desc
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294
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295
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296 def splitStrands(text, strand="+"):
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297 # positive_strands = []
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298 # negative_strands = []
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299 if strand == "+":
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300 if re.search(("(\[1\])"), text):
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301 return text
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302 elif strand == "-":
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303 if re.search(("(\[-1\])"), text):
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304 return text
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305 # return positive_strands, negative_strands
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306
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307
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308 def parse_a_range(pair, start, end):
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309 """
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310 Takes an input data tuple from a fasta tuple pair and keeps only those within the input sequence range
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311 ---> data : fasta tuple data
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312 ---> start : start range to keep
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313 ---> end : end range to keep (will need to + 1)
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314 """
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315 matches = []
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316 for each_pair in pair:
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317
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318 s = re.search(("[\d]+\.\."), each_pair[0]).group(0) # Start of the sequence
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319 s = int(s.split("..")[0])
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320 e = re.search(("\.\.[\d]+"), each_pair[0]).group(0)
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321 e = int(e.split("..")[1])
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322 if start - 1 <= s and e <= end + 1:
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323 matches.append(each_pair)
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324 else:
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325 continue
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326 # else:
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327 # continue
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328 # if matches != []:
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329 return matches
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330 # else:
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331 # print('no candidates within selected range')
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332
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333
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334 def grabLocs(text):
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335 """
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336 Grabs the locations of the spanin based on NT location (seen from ORF). Grabs the ORF name, as per named from the ORF class/module
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337 from cpt.py
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338 """
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339 start = re.search(("[\d]+\.\."), text).group(
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340 0
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341 ) # Start of the sequence ; looks for [numbers]..
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342 end = re.search(("\.\.[\d]+"), text).group(
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343 0
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344 ) # End of the sequence ; Looks for ..[numbers]
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345 orf = re.search(("(ORF)[\d]+"), text).group(
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346 0
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diff changeset
347 ) # Looks for ORF and the numbers that are after it
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
348 if re.search(("(\[1\])"), text): # stores strand
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
349 strand = "+"
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cpt
parents:
diff changeset
350 elif re.search(("(\[-1\])"), text): # stores strand
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
351 strand = "-"
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cpt
parents:
diff changeset
352 start = int(start.split("..")[0])
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
353 end = int(end.split("..")[1])
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
354 vals = [start, end, orf, strand]
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cpt
parents:
diff changeset
355
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
356 return vals
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cpt
parents:
diff changeset
357
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
358
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
359 def spaninProximity(isp, osp, max_dist=30):
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
360 """
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
361 _NOTE THIS FUNCTION COULD BE MODIFIED TO RETURN SEQUENCES_
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
362 Compares the locations of i-spanins and o-spanins. max_dist is the distance in NT measurement from i-spanin END site
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
363 to o-spanin START. The user will be inputting AA distance, so a conversion will be necessary (<user_input> * 3)
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
364 I modified this on 07.30.2020 to bypass the pick + or - strand. To
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
365 INPUT: list of OSP and ISP candidates
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
366 OUTPUT: Return (improved) candidates for overlapping, embedded, and separate list
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
367 """
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
368
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cpt
parents:
diff changeset
369 embedded = {}
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cpt
parents:
diff changeset
370 overlap = {}
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cpt
parents:
diff changeset
371 separate = {}
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cpt
parents:
diff changeset
372 for iseq in isp:
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
373 embedded[iseq[2]] = []
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
374 overlap[iseq[2]] = []
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
375 separate[iseq[2]] = []
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
376 for oseq in osp:
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cpt
parents:
diff changeset
377 if iseq[3] == "+":
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
378 if oseq[3] == "+":
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
379 if iseq[0] < oseq[0] < iseq[1] and oseq[1] < iseq[1]:
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
380 ### EMBEDDED ###
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
381 combo = [
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
382 iseq[0],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
383 iseq[1],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
384 oseq[2],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
385 oseq[0],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
386 oseq[1],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
387 iseq[3],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
388 ] # ordering a return for dic
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
389 embedded[iseq[2]] += [combo]
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
390 elif iseq[0] < oseq[0] <= iseq[1] and oseq[1] > iseq[1]:
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
391 ### OVERLAP / SEPARATE ###
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
392 if (iseq[1] - oseq[0]) < 6:
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
393 combo = [
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
394 iseq[0],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
395 iseq[1],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
396 oseq[2],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
397 oseq[0],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
398 oseq[1],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
399 iseq[3],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
400 ]
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
401 separate[iseq[2]] += [combo]
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
402 else:
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
403 combo = [
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
404 iseq[0],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
405 iseq[1],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
406 oseq[2],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
407 oseq[0],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
408 oseq[1],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
409 iseq[3],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
410 ]
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
411 overlap[iseq[2]] += [combo]
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
412 elif iseq[1] <= oseq[0] <= iseq[1] + max_dist:
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
413 combo = [iseq[0], iseq[1], oseq[2], oseq[0], oseq[1], iseq[3]]
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
414 separate[iseq[2]] += [combo]
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
415 else:
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
416 continue
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
417 if iseq[3] == "-":
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
418 if oseq[3] == "-":
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
419 if iseq[0] <= oseq[1] <= iseq[1] and oseq[0] > iseq[0]:
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
420 ### EMBEDDED ###
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
421 combo = [
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
422 iseq[0],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
423 iseq[1],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
424 oseq[2],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
425 oseq[0],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
426 oseq[1],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
427 iseq[3],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
428 ] # ordering a return for dict
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
429 embedded[iseq[2]] += [combo]
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
430 elif iseq[0] <= oseq[1] <= iseq[1] and oseq[0] < iseq[0]:
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
431 if (oseq[1] - iseq[0]) < 6:
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
432 combo = [
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
433 iseq[0],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
434 iseq[1],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
435 oseq[2],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
436 oseq[0],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
437 oseq[1],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
438 iseq[3],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
439 ]
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
440 separate[iseq[2]] += [combo]
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
441 else:
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
442 combo = [
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
443 iseq[0],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
444 iseq[1],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
445 oseq[2],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
446 oseq[0],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
447 oseq[1],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
448 iseq[3],
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
449 ]
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
450 overlap[iseq[2]] += [combo]
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
451 elif iseq[0] - 10 < oseq[1] < iseq[0]:
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
452 combo = [iseq[0], iseq[1], oseq[2], oseq[0], oseq[1], iseq[3]]
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
453 separate[iseq[2]] += [combo]
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
454 else:
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
455 continue
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
456
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
457 embedded = {k: embedded[k] for k in embedded if embedded[k]}
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
458 overlap = {k: overlap[k] for k in overlap if overlap[k]}
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
459 separate = {k: separate[k] for k in separate if separate[k]}
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
460
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
461 return embedded, overlap, separate
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
462
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
463
4e02e6e9e77d planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
464 def check_for_usp():
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465 "pass"
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466
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467
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468 ############################################### TEST RANGE #########################################################################
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469 ####################################################################################################################################
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470 if __name__ == "__main__":
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471
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472 #### TMD TEST
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473 test_desc = ["one", "two", "three", "four", "five"]
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474 test_seq = [
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475 "XXXXXXXXXXXXXXXFMCFMCFMCFMCFMCXXXXXXXXXXXXXXXXXXXXXXXXXX",
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476 "XXXXXXXXAAKKKKKKKKKKKKKKKXXXXXXXXXXXXX",
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477 "XXXXXXX",
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478 "XXXXXXXXXXXKXXXXXXXXXX",
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479 "XXXXXXXXXXAKXXXXXXXXXXAKXXXXXXXX",
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480 ]
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481 # for l in
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482 # combo = zip(test_desc,test_seq)
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483 pairs = zip(test_desc, test_seq)
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484 tmd = []
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485 for each_pair in pairs:
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486 # print(each_pair)
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487 try:
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488 tmd += find_tmd(pair=each_pair)
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489 except (IndexError, TypeError):
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490 continue
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491 # try:s = each_pair[1]
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492 # tmd += find_tmd(seq=s, tmsize=15)
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493 # print('\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n')
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494 # print(tmd)
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495 # print('\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n')
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496
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497 #### tuple-fasta TEST
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498 # fasta_file = 'out_isp.fa'
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499 # ret = tuple_fasta(fasta_file)
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500 # print('=============')
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501 # for i in ret:
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502 # print(i[1])
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503
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504 #### LipoBox TEST
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505 test_desc = ["one", "two", "three", "four", "five", "six", "seven"]
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506 test_seq = [
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507 "XXXXXXXXXTGGCXXXXXXXXXXXXXXXX",
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508 "XXXXXXXXAAKKKKKKKKKKKKKKKXXXXXXXXXXXXX",
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509 "XXXXXXX",
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510 "AGGCXXXXXXXXXXXXXXXXXXXXTT",
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511 "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTGGC",
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512 "XXXXXXXXXXXXXXXXXXXXXXXXXXTGGC",
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513 "MSTLRELRLRRALKEQSMRYLLSIKKTLPRWKGALIGLFLICVATISGCASESKLPEPPMVSVDSSLMVEPNLTTEMLNVFSQ*",
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514 ]
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515 pairs = zip(test_desc, test_seq)
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516 lipo = []
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517 for each_pair in pairs:
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518 # print(each_pair)
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519 # try:
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520 try:
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521 lipo += find_lipobox(pair=each_pair, regex=2) # , minimum=8)
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522 except TypeError: # catches if something doesnt have the min/max requirements (something is too small)
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523 continue
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524 # except:
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525 # continue
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526 # print('\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n')
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527 #############################3
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528 # g = prep_a_gff3(fa='putative_isp.fa', spanin_type='isp')
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529 # print(g)
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530 # write_gff3(data=g)