Mercurial > repos > cpt > cpt_find_spanins

annotate spaninFuncs.py @ 8:bf32db94fe46 draft default tip

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planemo upload commit cd3216893a76b4b9485c2615448b41dbf7133107
author cpt
date Fri, 20 Sep 2024 05:17:06 +0000
parents 46b252c89e9e
children
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3
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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
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11 # 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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12 # Much of the manipulation is string based; so it should be straightforward as well as moderately quick
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13 ################## GLobal Variables
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14 Lys = "K"
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15
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16
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17 def check_back_end_snorkels(seq, tmsize):
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18 """
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19 Searches through the backend of a potential TMD snorkel. This is the 2nd part of a TMD snorkel lysine match.
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20 --> seq : should be the sequence fed from the "search_region" portion of the sequence
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21 --> tmsize : size of the potential TMD being investigated
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22 """
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23 found = []
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24 if seq[tmsize - 4] == Lys and re.search(("[FIWLVMYCATGS]"), seq[tmsize - 5]):
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25 found = "match"
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26 return found
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27 elif seq[tmsize - 3] == Lys and re.search(("[FIWLVMYCATGS]"), seq[tmsize - 4]):
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28 found = "match"
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29 return found
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30 elif seq[tmsize - 2] == Lys and re.search(("[FIWLVMYCATGS]"), seq[tmsize - 3]):
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31 found = "match"
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32 return found
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33 elif seq[tmsize - 1] == Lys and re.search(("[FIWLVMYCATGS]"), seq[tmsize - 2]):
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34 found = "match"
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35 return found
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36 else:
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37 found = "NOTmatch"
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38 return found
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39
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40
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41 def prep_a_gff3(fa, spanin_type, org):
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42 """
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43 Function parses an input detailed 'fa' file and outputs a 'gff3' file
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44 ---> fa = input .fa file
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45 ---> output = output a returned list of data, easily portable to a gff3 next
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46 ---> spanin_type = 'isp' or 'osp'
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47 """
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48 with org as f:
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49 header = f.readline()
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50 orgacc = header.split(" ")
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51 orgacc = orgacc[0].split(">")[1].strip()
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52 fa_zip = tuple_fasta(fa)
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53 data = []
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54 for a_pair in fa_zip:
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55 # print(a_pair)
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56 if re.search(("(\[1\])"), a_pair[0]):
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57 strand = "+"
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58 elif re.search(("(\[-1\])"), a_pair[0]):
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59 strand = "-" # column 7
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60 start = re.search(("[\d]+\.\."), a_pair[0]).group(0).split("..")[0] # column 4
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61 end = re.search(("\.\.[\d]+"), a_pair[0]).group(0).split("..")[1] # column 5
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62 orfid = re.search(("(ORF)[\d]+"), a_pair[0]).group(0) # column 1
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63 if spanin_type == "isp":
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64 methodtype = "CDS" # column 3
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65 spanin = "isp"
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66 elif spanin_type == "osp":
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67 methodtype = "CDS" # column 3
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68 spanin = "osp"
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69 elif spanin_type == "usp":
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70 methodtype = "CDS"
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71 spanin = "usp"
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72 else:
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73 raise "need to input spanin type"
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74 source = "cpt.py|putative-*.py" # column 2
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75 score = "." # column 6
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76 phase = "." # column 8
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77 attributes = (
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78 "ID=" + orgacc + "|" + orfid + ";ALIAS=" + spanin + ";SEQ=" + a_pair[1]
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79 ) # column 9
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80 sequence = [
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81 [orgacc, source, methodtype, start, end, score, strand, phase, attributes]
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82 ]
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83 data += sequence
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84 return data
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85
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86
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87 def write_gff3(data, output="results.gff3"):
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88 """
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89 Parses results from prep_a_gff3 into a gff3 file
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90 ---> input : list from prep_a_gff3
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91 ---> output : gff3 file
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92 """
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93 data = data
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94 filename = output
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95 with filename as f:
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96 f.write("#gff-version 3\n")
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97 for value in data:
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98 f.write(
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99 "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(
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100 value[0],
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101 value[1],
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102 value[2],
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103 value[3],
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104 value[4],
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105 value[5],
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106 value[6],
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107 value[7],
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108 value[8],
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109 )
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110 )
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111 f.close()
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112
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113
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114 def find_tmd(
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115 pair,
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116 minimum=10,
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117 maximum=30,
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118 TMDmin=10,
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119 TMDmax=20,
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120 isp_mode=False,
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121 peri_min=18,
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122 peri_max=206,
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123 ):
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124 """
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125 Function that searches for lysine snorkels and then for a spanning hydrophobic region that indicates a potential TMD
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126 ---> pair : Input of tuple with description and AA sequence (str)
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127 ---> minimum : How close from the initial start codon a TMD can be within
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128 ---> maximum : How far from the initial start codon a TMD can be within
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129 ---> TMDmin : The minimum size that a transmembrane can be (default = 10)
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130 ---> TMDmax : The maximum size tha ta transmembrane can be (default = 20)
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131 """
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132 # hydrophobicAAs = ['P', 'F', 'I', 'W', 'L', 'V', 'M', 'Y', 'C', 'A', 'T', 'G', 'S']
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133 tmd = []
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134 s = str(pair[1]) # sequence being analyzed
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135 # print(s) # for trouble shooting
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136 if maximum > len(s):
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137 maximum = len(s)
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138 search_region = s[minimum - 1 : maximum + 1]
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139 # print(f"this is the search region: {search_region}")
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140 # print(search_region) # for trouble shooting
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141
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142 for tmsize in range(TMDmin, TMDmax + 1, 1):
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143 # print(f"this is the current tmsize we're trying: {tmsize}")
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144 # print('==============='+str(tmsize)+'================') # print for troubleshooting
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145 pattern = (
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146 "[PFIWLVMYCATGS]{" + str(tmsize) + "}"
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147 ) # searches for these hydrophobic residues tmsize total times
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148 # print(pattern)
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149 # print(f"sending to regex: {search_region}")
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150 if re.search(
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151 ("[K]"), search_region[1:8]
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152 ): # grabbing one below with search region, so I want to grab one ahead here when I query.
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153 store_search = re.search(
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154 ("[K]"), search_region[1:8]
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155 ) # storing regex object
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156 where_we_are = store_search.start() # finding where we got the hit
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157 if re.search(
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158 ("[PFIWLVMYCATGS]"), search_region[where_we_are + 1]
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159 ) and re.search(
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160 ("[PFIWLVMYCATGS]"), search_region[where_we_are - 1]
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161 ): # hydrophobic neighbor
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162 # try:
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163 g = re.search(
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164 ("[PFIWLVMYCATGS]"), search_region[where_we_are + 1]
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165 ).group()
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166 backend = check_back_end_snorkels(search_region, tmsize)
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167 if backend == "match":
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168 if isp_mode:
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169 g = re.search((pattern), search_region).group()
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170 end_of_tmd = re.search((g), s).end() + 1
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171 amt_peri = len(s) - end_of_tmd
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172 if peri_min <= amt_peri <= peri_max:
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173 pair_desc = pair[0] + ", peri_count~=" + str(amt_peri)
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174 new_pair = (pair_desc, pair[1])
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175 tmd.append(new_pair)
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176 else:
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177 tmd.append(pair)
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178 else:
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179 continue
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180 # else:
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181 # print("I'm continuing out of snorkel loop")
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182 # print(f"{search_region}")
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183 # continue
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184 if re.search((pattern), search_region):
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185 # print(f"found match: {}")
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186 # print("I AM HEREEEEEEEEEEEEEEEEEEEEEEE")
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187 # try:
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188 if isp_mode:
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189 g = re.search((pattern), search_region).group()
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190 end_of_tmd = re.search((g), s).end() + 1
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191 amt_peri = len(s) - end_of_tmd
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192 if peri_min <= amt_peri <= peri_max:
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193 pair_desc = pair[0] + ", peri_count~=" + str(amt_peri)
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194 new_pair = (pair_desc, pair[1])
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195 tmd.append(new_pair)
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196 else:
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197 tmd.append(pair)
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198 else:
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199 continue
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200
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201 return tmd
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202
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203
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204 def find_lipobox(
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205 pair, minimum=10, maximum=50, min_after=30, max_after=185, regex=1, osp_mode=False
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206 ):
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207 """
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208 Function that takes an input tuple, and will return pairs of sequences to their description that have a lipoobox
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209 ---> minimum - min distance from start codon to first AA of lipobox
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210 ---> maximum - max distance from start codon to first AA of lipobox
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211 ---> regex - option 1 (default) => more strict regular expression ; option 2 => looser selection, imported from LipoRy
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212
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213 """
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214 if regex == 1:
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215 pattern = "[ILMFTV][^REKD][GAS]C" # regex for Lipobox from findSpanin.pl
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216 elif regex == 2:
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217 pattern = "[ACGSILMFTV][^REKD][GAS]C" # regex for Lipobox from LipoRy
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218
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219 candidates = []
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220 s = str(pair[1])
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221 # print(s) # trouble shooting
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222 search_region = s[
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223 minimum - 1 : maximum + 5
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224 ] # properly slice the input... add 4 to catch if it hangs off at max input
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225 # print(search_region) # trouble shooting
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226 patterns = ["[ILMFTV][^REKD][GAS]C", "AW[AGS]C"]
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227 for pattern in patterns:
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228 # print(pattern) # trouble shooting
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229 if re.search((pattern), search_region): # lipobox must be WITHIN the range...
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230 # searches the sequence with the input RegEx AND omits if
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231 g = re.search(
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232 (pattern), search_region
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233 ).group() # find the exact group match
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234 amt_peri = len(s) - re.search((g), s).end() + 1
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235 if min_after <= amt_peri <= max_after: # find the lipobox end region
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236 if osp_mode:
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237 pair_desc = pair[0] + ", peri_count~=" + str(amt_peri)
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238 new_pair = (pair_desc, pair[1])
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239 candidates.append(new_pair)
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240 else:
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241 candidates.append(pair)
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242
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243 return candidates
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244
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245
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246 def tuple_fasta(fasta_file):
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247 """
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248 #### INPUT: Fasta File
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249 #### OUTPUT: zipped (zip) : pairwise relationship of description to sequence
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250 ####
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251 """
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252 fasta = SeqIO.parse(fasta_file, "fasta")
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253 descriptions = []
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254 sequences = []
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255 for r in fasta: # iterates and stores each description and sequence
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256 description = r.description
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257 sequence = str(r.seq)
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258 if (
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259 sequence[0] != "I"
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260 ): # the translation table currently has I as a potential start codon ==> this will remove all ORFs that start with I
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261 descriptions.append(description)
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262 sequences.append(sequence)
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263 else:
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264 continue
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265
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266 return zip(descriptions, sequences)
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267
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268
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269 def lineWrapper(text, charactersize=60):
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270
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271 if len(text) <= charactersize:
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272 return text
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273 else:
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274 return (
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275 text[:charactersize]
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276 + "\n"
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277 + lineWrapper(text[charactersize:], charactersize)
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278 )
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279
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280
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281 def getDescriptions(fasta):
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282 """
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283 Takes an output FASTA file, and parses retrieves the description headers. These headers contain information needed
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284 for finding locations of a potential i-spanin and o-spanin proximity to one another.
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285 """
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286 desc = []
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287 with fasta as f:
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288 for line in f:
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289 if line.startswith(">"):
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290 desc.append(line)
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291 return desc
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292
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293
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294 def splitStrands(text, strand="+"):
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295 # positive_strands = []
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296 # negative_strands = []
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297 if strand == "+":
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298 if re.search(("(\[1\])"), text):
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299 return text
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300 elif strand == "-":
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301 if re.search(("(\[-1\])"), text):
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302 return text
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303 # return positive_strands, negative_strands
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304
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305
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306 def parse_a_range(pair, start, end):
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307 """
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308 Takes an input data tuple from a fasta tuple pair and keeps only those within the input sequence range
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309 ---> data : fasta tuple data
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310 ---> start : start range to keep
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311 ---> end : end range to keep (will need to + 1)
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312 """
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313 matches = []
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314 for each_pair in pair:
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315
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316 s = re.search(("[\d]+\.\."), each_pair[0]).group(0) # Start of the sequence
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317 s = int(s.split("..")[0])
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318 e = re.search(("\.\.[\d]+"), each_pair[0]).group(0)
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319 e = int(e.split("..")[1])
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320 if start - 1 <= s and e <= end + 1:
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321 matches.append(each_pair)
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322 else:
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323 continue
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324 # else:
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325 # continue
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326 # if matches != []:
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327 return matches
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328 # else:
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329 # print('no candidates within selected range')
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330
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331
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332 def grabLocs(text):
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333 """
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334 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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335 from cpt.py
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336 """
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337 start = re.search(("[\d]+\.\."), text).group(
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338 0
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339 ) # Start of the sequence ; looks for [numbers]..
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340 end = re.search(("\.\.[\d]+"), text).group(
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341 0
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342 ) # End of the sequence ; Looks for ..[numbers]
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343 orf = re.search(("(ORF)[\d]+"), text).group(
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344 0
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345 ) # Looks for ORF and the numbers that are after it
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346 if re.search(("(\[1\])"), text): # stores strand
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347 strand = "+"
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348 elif re.search(("(\[-1\])"), text): # stores strand
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349 strand = "-"
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350 start = int(start.split("..")[0])
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351 end = int(end.split("..")[1])
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352 vals = [start, end, orf, strand]
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353
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354 return vals
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355
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356
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357 def spaninProximity(isp, osp, max_dist=30):
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358 """
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359 _NOTE THIS FUNCTION COULD BE MODIFIED TO RETURN SEQUENCES_
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360 Compares the locations of i-spanins and o-spanins. max_dist is the distance in NT measurement from i-spanin END site
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361 to o-spanin START. The user will be inputting AA distance, so a conversion will be necessary (<user_input> * 3)
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362 I modified this on 07.30.2020 to bypass the pick + or - strand. To
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363 INPUT: list of OSP and ISP candidates
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364 OUTPUT: Return (improved) candidates for overlapping, embedded, and separate list
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365 """
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366
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367 embedded = {}
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368 overlap = {}
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diff changeset
369 separate = {}
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
370 for iseq in isp:
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
371 embedded[iseq[2]] = []
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
372 overlap[iseq[2]] = []
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
373 separate[iseq[2]] = []
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
374 for oseq in osp:
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
375 if iseq[3] == "+":
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
376 if oseq[3] == "+":
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
377 if iseq[0] < oseq[0] < iseq[1] and oseq[1] < iseq[1]:
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
378 ### EMBEDDED ###
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
379 combo = [
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
380 iseq[0],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
381 iseq[1],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
382 oseq[2],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
383 oseq[0],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
384 oseq[1],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
385 iseq[3],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
386 ] # ordering a return for dic
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
387 embedded[iseq[2]] += [combo]
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
388 elif iseq[0] < oseq[0] <= iseq[1] and oseq[1] > iseq[1]:
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
389 ### OVERLAP / SEPARATE ###
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
390 if (iseq[1] - oseq[0]) < 6:
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
391 combo = [
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
392 iseq[0],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
393 iseq[1],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
394 oseq[2],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
395 oseq[0],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
396 oseq[1],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
397 iseq[3],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
398 ]
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
399 separate[iseq[2]] += [combo]
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
400 else:
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
401 combo = [
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
402 iseq[0],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
403 iseq[1],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
404 oseq[2],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
405 oseq[0],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
406 oseq[1],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
407 iseq[3],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
408 ]
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
409 overlap[iseq[2]] += [combo]
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
410 elif iseq[1] <= oseq[0] <= iseq[1] + max_dist:
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
411 combo = [iseq[0], iseq[1], oseq[2], oseq[0], oseq[1], iseq[3]]
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
412 separate[iseq[2]] += [combo]
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
413 else:
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
414 continue
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
415 if iseq[3] == "-":
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
416 if oseq[3] == "-":
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
417 if iseq[0] <= oseq[1] <= iseq[1] and oseq[0] > iseq[0]:
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
418 ### EMBEDDED ###
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
419 combo = [
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
420 iseq[0],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
421 iseq[1],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
422 oseq[2],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
423 oseq[0],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
424 oseq[1],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
425 iseq[3],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
426 ] # ordering a return for dict
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
427 embedded[iseq[2]] += [combo]
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
428 elif iseq[0] <= oseq[1] <= iseq[1] and oseq[0] < iseq[0]:
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
429 if (oseq[1] - iseq[0]) < 6:
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
430 combo = [
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
431 iseq[0],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
432 iseq[1],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
433 oseq[2],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
434 oseq[0],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
435 oseq[1],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
436 iseq[3],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
437 ]
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
438 separate[iseq[2]] += [combo]
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
439 else:
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
440 combo = [
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
441 iseq[0],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
442 iseq[1],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
443 oseq[2],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
444 oseq[0],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
445 oseq[1],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
446 iseq[3],
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
447 ]
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
448 overlap[iseq[2]] += [combo]
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
449 elif iseq[0] - 10 < oseq[1] < iseq[0]:
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
450 combo = [iseq[0], iseq[1], oseq[2], oseq[0], oseq[1], iseq[3]]
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
451 separate[iseq[2]] += [combo]
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
452 else:
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
453 continue
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
454
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
455 embedded = {k: embedded[k] for k in embedded if embedded[k]}
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
456 overlap = {k: overlap[k] for k in overlap if overlap[k]}
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
457 separate = {k: separate[k] for k in separate if separate[k]}
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
458
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
459 return embedded, overlap, separate
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
460
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
461
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
462 def check_for_usp():
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
463 "pass"
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
464
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
465
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
466 ############################################### TEST RANGE #########################################################################
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
467 ####################################################################################################################################
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
468 if __name__ == "__main__":
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
469
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
470 #### TMD TEST
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
471 test_desc = ["one", "two", "three", "four", "five"]
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
472 test_seq = [
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
473 "XXXXXXXXXXXXXXXFMCFMCFMCFMCFMCXXXXXXXXXXXXXXXXXXXXXXXXXX",
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
474 "XXXXXXXXAAKKKKKKKKKKKKKKKXXXXXXXXXXXXX",
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
475 "XXXXXXX",
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
476 "XXXXXXXXXXXKXXXXXXXXXX",
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
477 "XXXXXXXXXXAKXXXXXXXXXXAKXXXXXXXX",
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
478 ]
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
479 # for l in
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
480 # combo = zip(test_desc,test_seq)
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
481 pairs = zip(test_desc, test_seq)
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
482 tmd = []
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
483 for each_pair in pairs:
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
484 # print(each_pair)
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
485 try:
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
486 tmd += find_tmd(pair=each_pair)
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
487 except (IndexError, TypeError):
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
488 continue
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
489 # try:s = each_pair[1]
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
490 # tmd += find_tmd(seq=s, tmsize=15)
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
491 # print('\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n')
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
492 # print(tmd)
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
493 # print('\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n')
fd70980a516b planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
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494
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495 #### tuple-fasta TEST
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496 # fasta_file = 'out_isp.fa'
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497 # ret = tuple_fasta(fasta_file)
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498 # print('=============')
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499 # for i in ret:
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500 # print(i[1])
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501
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502 #### LipoBox TEST
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503 test_desc = ["one", "two", "three", "four", "five", "six", "seven"]
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504 test_seq = [
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505 "XXXXXXXXXTGGCXXXXXXXXXXXXXXXX",
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506 "XXXXXXXXAAKKKKKKKKKKKKKKKXXXXXXXXXXXXX",
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507 "XXXXXXX",
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508 "AGGCXXXXXXXXXXXXXXXXXXXXTT",
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509 "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTGGC",
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510 "XXXXXXXXXXXXXXXXXXXXXXXXXXTGGC",
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511 "MSTLRELRLRRALKEQSMRYLLSIKKTLPRWKGALIGLFLICVATISGCASESKLPEPPMVSVDSSLMVEPNLTTEMLNVFSQ*",
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512 ]
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513 pairs = zip(test_desc, test_seq)
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514 lipo = []
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515 for each_pair in pairs:
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516 # print(each_pair)
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517 # try:
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518 try:
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519 lipo += find_lipobox(pair=each_pair, regex=2) # , minimum=8)
5
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520 except (
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521 TypeError
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522 ): # catches if something doesnt have the min/max requirements (something is too small)
3
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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)