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annotate MolD_v1.4.py @ 0:4e8e2f836d0f draft default tip

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planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
author itaxotools
date Sun, 29 Jan 2023 16:25:48 +0000
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1 """
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2 This script compiles rDNC-based DNA diagnoses for a pre-defined taxa in a dataset. This is the MAIN WORKING VERSION v1.4
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3 This version already implements the new functionalities:
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4 - automatic trimming of the alignment to match the median sequence length (should seq len distribution and provided NumberN settings require that)
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5 - expanded qCLADEs setting
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6 - diagnoses in pairwise comparisons of taxa.
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7 - selection of a reference sequence for indexing DNCs
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8
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9 THIS version LACKS SPART compatibility
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10
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11 """
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12 import os, sys
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13 import random
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14 import argparse
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15 from io import StringIO
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16 ######################################################################## FUNCTIONS
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17 #***STEP 1 - SORTING ENTRIES BY CLADE AND IDENTIFYING NUCLEOTIDE POSITIONS SHARED WITHIN CLADE
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18 def Step1(raw_records):
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19 Clades=[]
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20 for i in range(len(raw_records)):
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21 Clade=raw_records[i][1]
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22 if Clade not in Clades:
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23 Clades.append(Clade)
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24 clade_sorted_seqs = {}
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25 for letter in Clades:
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26 clade_sorted_seqs[letter]=[]
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27 for i in range(len(raw_records)):
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28 if raw_records[i][1]==letter:
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29 clade_sorted_seqs[letter].append(raw_records[i][2])
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30 shared_positions={}
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31 for key in clade_sorted_seqs:
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32 sh_pos=[]
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33 for i in range(len(clade_sorted_seqs[key][0])):
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34 shared_nucleotide = True
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35 csm = clade_sorted_seqs[key][0][i] #candidate shared nucleotide
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36 for j in range(1, len(clade_sorted_seqs[key])):
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37 if clade_sorted_seqs[key][j][i] != csm:
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38 shared_nucleotide = False
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39 break
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40 if shared_nucleotide == True and csm != 'N':
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41 sh_pos.append(i)
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42 shared_positions[key]=sh_pos
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43 return Clades, clade_sorted_seqs, shared_positions
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44
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45 #***STEP 2 COMPILING COMPARISON LISTS FOR CLADES AND IDENTIFYING VARIABLE POSITIONS AND N PRIORITY POSITIONS WITH LARGEST CUTOFFS
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46 def C_VP_PP(clade_sorted_seqs, clade, shared_positions, CUTOFF):# complist_variable_positions_priority_positions; Arguments: dictionary, string, dictionary
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47 CShN={}#a dictionary keys - clade shared positions, values - nucleotides at those positions
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48 for pos in shared_positions[clade]:
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49 CShN[pos] = clade_sorted_seqs[clade][0][pos]#creates a dictionary shared position : nucleotide
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50 complist=[]
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51 for key in clade_sorted_seqs:
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52 if key != clade:
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53 complist = complist + clade_sorted_seqs[key]#creates a list of all other sequences for comparison
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54 cutoffs = {}
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55 pures = []####! newline
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56 for key in CShN:
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57 newcomplist = []
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58 for k in complist:
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59 if k[key] == CShN[key]:
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60 newcomplist.append(k)
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61 else: continue
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62 cutoffs[key] = len(complist) - len(newcomplist)
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63 if len(newcomplist) == 0:####! newline
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64 pures.append(key)####! newline
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65 CPP = []
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66 for key in sorted(cutoffs, key = cutoffs.get, reverse = True):
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67 CPP.append(key)
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68 if CUTOFF[0] == '>':#VERYNEW
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69 Clade_priority_positions = {pos:CShN[pos] for pos in CPP if cutoffs[pos] > int(CUTOFF[1:])}#VERYNEW
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70 else:#VERYNEW
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71 Clade_priority_positions = {}
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72 for position in CPP[:int(CUTOFF)]:#Here you define how many of the clade shared combinations are used in subsequent search
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73 Clade_priority_positions[position] = CShN[position]
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74 return complist, Clade_priority_positions, cutoffs, pures####! pures added
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75
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76 #***STEPS 3 RANDOM SEARCH ACROSS PRIORITY POSITIONS TO FIND RAW DIAGNOSTIC COMBINATIONS AND TO SUBSEQUENTLY REFINE THEM
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77 def random_position(somelist, checklist):#gives a random index (integer) of the specified range, and returns indexed somelist element if it is not present in the checklist
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78 while True:
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79 i = random.randint(0, len(somelist) - 1)
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80 if somelist[i] not in checklist:
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81 return somelist[i]
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82 break
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83 else:
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84 continue
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85
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86 def step_reduction_complist(clade, complist, CPP, checked_ind):#checks randomly selected positions of CladeSharedNucleotides with sequences of other clades, until a diagnostic combination of nucleotides for a selected clade is found.
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87 if len(complist) == 0:
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88 return checked_ind
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89 elif len(checked_ind) == len(CPP):
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90 return checked_ind
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91 else:
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92 newcomplist = []
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93 pos = random_position(list(CPP.keys()), checked_ind)
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94 for j in complist:
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95 if j[pos] == CPP[pos] or j[pos] == 'N':#VERYNEW
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96 newcomplist.append(j)
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97 else: continue
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98 new_checked_ind = checked_ind + [pos]
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99 return step_reduction_complist(clade, newcomplist, CPP, new_checked_ind)
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100
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101 def ConditionD(newcomb, complist, CPP):#The function checks the 'Condition D' - i.e. whither any given combination of nucleotide positions is diagnostic for the selected clade
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102 ContD = False
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103 for i in newcomb:
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104 newcomplist = []
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105 for m in complist:
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106 if m[i] == CPP[i]:
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107 newcomplist.append(m)
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108 else: continue
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109 complist = newcomplist
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110 if len(complist) == 0:
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111 ContD = True
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112 return ContD
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113
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114 def RemoveRedundantPositions(raw_comb, complist, CPP):# The function removes positions from the raw combinations one by one, and then checks whether new combination fulfills the condition D, thus recursively reducing the diagnostic combination.
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115 red_possible = False
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116 for j in raw_comb:
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117 newcomb = [k for k in raw_comb if k != j]
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118 if ConditionD(newcomb, complist, CPP) == True:
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119 red_possible = True
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120 return RemoveRedundantPositions(newcomb, complist, CPP)
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121 else: pass
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122 if red_possible == False:
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123 return raw_comb
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124
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125 #PUTS EVERYTHING TOGETHER - 20000 ROUNDS OF RANDOM SEARCH FOLLOWED BY REFINING OF 500 SHORTEST COMBINATIONS
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126 def Diagnostic_combinations(qCLADE, complist, CPP, n1, maxlen1, maxlen2):
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127 Achecked_ind = []
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128 bestlists = []
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129 n = n1
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130 while n>0:#STEP3 proposes raw diagnostic combinations
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131 raw_comb = step_reduction_complist(qCLADE, complist, CPP, Achecked_ind)
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132 if len(raw_comb) <= maxlen1:
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133 refined_comb = RemoveRedundantPositions(raw_comb, complist, CPP)
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134 if len(refined_comb) <= maxlen2 and sorted(refined_comb) not in bestlists:
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135 bestlists.append(sorted(refined_comb))
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136 n=n-1
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137 bestlists.sort(key=len)
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138 return bestlists
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139
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140 #***STEP 4 ANALYSIS OF OUTPUT rDNCs
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141 def IndependentKey(diagnostic_combinations):#PRESENTLY NOT INVOLVED - returns independent diagnostic nucleotide combinations, and identifies key nucleotide positions
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142 independent_combinations = []
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143 selected_positions = []
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144 for i in range(len(diagnostic_combinations)):
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145 if len(selected_positions) == 0:
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146 for j in range(0, i):
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147 if len(set(diagnostic_combinations[i]) & set(diagnostic_combinations[j])) == 0 and len(set(diagnostic_combinations[i]) & set(selected_positions)) == 0:
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148 independent_combinations.append(diagnostic_combinations[i])
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149 independent_combinations.append(diagnostic_combinations[j])
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150 for k in range(len(diagnostic_combinations[i])):
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151 selected_positions.append(diagnostic_combinations[i][k])
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152 for l in range(len(diagnostic_combinations[j])):
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153 selected_positions.append(diagnostic_combinations[j][l])
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154 else:
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155 if len(set(diagnostic_combinations[i]) & set(selected_positions)) == 0:
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156 independent_combinations.append(diagnostic_combinations[i])
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157 for k in range(len(diagnostic_combinations[i])):
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158 selected_positions.append(diagnostic_combinations[i][k])
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159 independent_combinations.sort(key=len)
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160 key_positions = []
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161 for pos in diagnostic_combinations[0]:
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162 KP = True
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163 for combination in diagnostic_combinations[1:]:
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164 if pos not in combination:
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165 KP = False
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166 break
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167 else: continue
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168 if KP == True:
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169 key_positions.append(pos)
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170 return independent_combinations, key_positions
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171
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172 #SPECIFIC FUNCTIONS FOR THE rDNCs
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173 def PositionArrays(Motifs):#VERYNEW ALL FUNCTION NEW
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174 PositionArrays = []
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175 VarPosList = []
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176 for i in range(len(Motifs[0])):
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177 Const = True
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178 array = [Motifs[0][i]]
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179 for j in range(len(Motifs[1:])):
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180 if Motifs[j][i] != 'N':
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181 if Motifs[j][i] != array[-1]:
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182 Const = False
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183 array.append(Motifs[j][i])
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184 PositionArrays.append(array)
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185 if Const == False:
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186 VarPosList.append(i)
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187 return PositionArrays, VarPosList
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188
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189 def random_sequence_new(SEQ, PositionArrays, VarPosList, Pdiff):#VERYNEW FUNCTION REVISED
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190 #print(["ROUND", len(SEQ)*Pdiff/100, round(len(SEQ)*Pdiff/100)])
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191 n = round(len(SEQ)*Pdiff/100)
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192 N = random.sample(list(range(1, n)), 1)[0]
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193 PosToChange = random.sample([p for p in VarPosList if SEQ[p] != 'D'], N)#this is a new definition to keep alignment gaps unchanged
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194 NEWSEQ = ''
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195 for i in range(len(SEQ)):
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196 if i not in PosToChange:
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197 NEWSEQ = NEWSEQ + SEQ[i]
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198 else:
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199 newarray = [j for j in PositionArrays[i] if j != SEQ[i]]
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200 newbase = random.sample(newarray, 1)[0]
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201 NEWSEQ = NEWSEQ + newbase
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202 return NEWSEQ
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203
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204 def GenerateBarcode_new(Diagnostic_combinations, length):#VERYNEW FUNCTION REVISED - This function calculates diagnostic combinations and assembles a barcode of desired length for a query taxon. First all single position DNCs are added, then based on the frequency of a nucleotide position in the DNCs of the 2 positions, and then based on the frequency of a position in longer DNCs
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205 len1 = []
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206 len2 = []
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207 lenmore = []
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208 for comb in Diagnostic_combinations:
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209 if len(comb) == len(Diagnostic_combinations[0]):
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210 for i in comb:
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211 len1.append(i)
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212 elif len(comb) == len(Diagnostic_combinations[0])+1:
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213 for j in comb:
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214 len2.append(j)
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215 else:
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216 for k in comb:
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217 lenmore.append(k)
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218 if len(Diagnostic_combinations[0]) == 1:
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219 Setin = len1
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220 else:
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221 Setin = []
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222 for pos in sorted(len1, key=len1.count, reverse = True):
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223 if not pos in Setin:
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224 Setin.append(pos)
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225 for pos1 in sorted(len2, key=len2.count, reverse = True):
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226 if not pos1 in Setin:
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227 Setin.append(pos1)
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228 for pos2 in sorted(lenmore, key=lenmore.count, reverse = True):
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229 if not pos2 in Setin:
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230 Setin.append(pos2)
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231 return Setin[:length]
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232
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233 def Screwed_dataset_new(raw_records, nseq_per_clade_to_screw, PositionArrays, VarPosList, Percent_difference, Taxon, Cutoff):#VERYNEW FUNCTION REVISED
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234 clades=[]
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235 for i in range(len(raw_records)):
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236 Clade=raw_records[i][1]
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237 if Clade not in clades:
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238 clades.append(Clade)
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239 clade_sorted_seqs = {}
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240 for letter in clades:
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241 clade_sorted_seqs[letter]=[]
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242 for i in range(len(raw_records)):
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243 if raw_records[i][1]==letter:
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244 clade_sorted_seqs[letter].append(raw_records[i][2])
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245
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246 for clade in clades:
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247 seqlist = clade_sorted_seqs[clade]
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248 newseqs = []
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249 if len(seqlist) > nseq_per_clade_to_screw:
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250 iSTS = random.sample(list(range(len(seqlist))), nseq_per_clade_to_screw)
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251 for k in range(len(seqlist)):
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252 if k in iSTS:
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253 newseq = random_sequence_new(seqlist[k], PositionArrays, VarPosList, Percent_difference)
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254 else:
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255 newseq = seqlist[k]
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256 newseqs.append(newseq)
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257 elif len(clade_sorted_seqs[clade]) == nseq_per_clade_to_screw:
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258 for k in range(len(seqlist)):
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259 newseq = random_sequence_new(seqlist[k], PositionArrays, VarPosList, Percent_difference)
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260 newseqs.append(newseq)
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261 else:
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262 for i in range(nseq_per_clade_to_screw):
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263 seq = random.sample(seqlist, 1)[0]
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264 newseq = random_sequence_new(seq, PositionArrays, VarPosList, Percent_difference)
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265 newseqs.append(newseq)
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266 clade_sorted_seqs[clade] = newseqs
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267
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268 shared_positions={}
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269 for key in clade_sorted_seqs:
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270 sh_pos=[]
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271 for i in range(len(clade_sorted_seqs[key][0])):
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272 shared_nucleotide = True
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273 csm = clade_sorted_seqs[key][0][i] #candidate shared nucleotide
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274 for j in range(1, len(clade_sorted_seqs[key])):
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275 if clade_sorted_seqs[key][j][i] != csm:
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276 shared_nucleotide = False
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277 break
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278 if shared_nucleotide == True and csm != 'N':
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279 sh_pos.append(i)
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280 shared_positions[key]=sh_pos
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281
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282 x,y,z,pures = C_VP_PP(clade_sorted_seqs, Taxon, shared_positions, Cutoff)#STEP2####
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283 return x, y
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284
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285 #NEWFUNCYIONS
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286 def medianSeqLen(listofseqs):#OCT2022
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287 seqlens = [i.count('A')+i.count('C')+i.count('G')+i.count('T') for i in listofseqs]
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288 medlen = sorted(seqlens)[int(len(seqlens)/2)]
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289 medseq = listofseqs[seqlens.index(medlen)]
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290 start = min([medseq.find('A'),medseq.find('C'),medseq.find('G'),medseq.count('T')])
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291 if not 'N' in medseq[start:]:
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292 end = len(medseq)
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293 else:
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294 for i in range(start, len(medseq), 1):
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295 if medseq[i:].count('N') == len(medseq[i:]):
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296 end = i
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297 break
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298 return medlen, start, end
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299
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300 def getAllPairs(taxalist):
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301 uniquetaxapairs = []
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302 stl = sorted(list(set(taxalist)))
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303 for i in range(len(stl)):
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304 for j in range(i+1, len(stl)):
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305 uniquetaxapairs.append([stl[i],stl[j]])
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306 return uniquetaxapairs
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307
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308
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309 ################################################READ IN PARAMETER FILE AND DATA FILE
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310
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311 def get_args(): #arguments needed to give to this script
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312 parser = argparse.ArgumentParser(description="run MolD")
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313 required = parser.add_argument_group("required arguments")
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314 required.add_argument("-i", help="textfile with parameters of the analysis", required=True)
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315 return parser.parse_args()
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316
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317 def mainprocessing(gapsaschars=None, taxalist=None, taxonrank=None, cutoff=None, numnucl=None, numiter=None, maxlenraw=None, maxlenrefined=None, iref=None, pdiff=None, nmax=None, thresh=None, tmpfname=None, origfname=None):
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318 ParDict = {}
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319 if not(all([gapsaschars, taxalist, taxonrank, cutoff, numnucl, numiter, maxlenraw, maxlenrefined, iref, pdiff, nmax, thresh, tmpfname])):
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320 args = get_args()
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321 with open(args.i) as params:
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322 for line in params:
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323 line = line.strip()
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324 if line.startswith('#'):
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325 pass
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326 else:
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327 if len(line.split('=')) == 2 and len(line.split('=')[1]) != 0:
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328 ParDict[line.split('=')[0]] = line.split('=')[1].replace(' ', '')#VERYNEW
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329 else:
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330 ParDict['Gaps_as_chars'] = gapsaschars
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331 ParDict['qTAXA'] = taxalist
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332 ParDict['Taxon_rank'] = taxonrank
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333 ParDict['INPUT_FILE'] = tmpfname
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334 ParDict['ORIG_FNAME'] = origfname# I do not understand this ORIG_FNAME, it throws an error with the command line
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335 ParDict['Cutoff'] = cutoff
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336 ParDict['NumberN'] = numnucl
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337 ParDict['Number_of_iterations'] = numiter
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338 ParDict['MaxLen1'] = maxlenraw
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339 ParDict['MaxLen2'] = maxlenrefined
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340 ParDict['Iref'] = iref
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341 ParDict['Pdiff'] = pdiff
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342 #ParDict['PrSeq'] = prseq
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343 ParDict['NMaxSeq'] = nmax
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344 ParDict['Scoring'] = thresh
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345 ParDict['OUTPUT_FILE'] = "str"
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346 print(ParDict)
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347 ############################################# #VERYNEW HOW GAPS ARE TREATED
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348 #REQUIRES A NEW FIELD IN THE GUI
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349 if ParDict['Gaps_as_chars'] == 'yes':
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350 gaps2D = True#VERYNEW
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351 else:#VERYNEW
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352 gaps2D = False#VERYNEW
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353
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diff changeset
354 ############################################ DATA FILE
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parents:
diff changeset
355 checkread = open(ParDict['INPUT_FILE'], 'r')
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parents:
diff changeset
356 firstline = checkread.readline()
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itaxotools
parents:
diff changeset
357 checkread.close()
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itaxotools
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diff changeset
358 imported=[]#set up a new list with species and identifiers
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itaxotools
parents:
diff changeset
359 if '>' in firstline:
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diff changeset
360 f = open(ParDict['INPUT_FILE'], 'r')
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diff changeset
361 for line in f:#VERYNEW - THE DATA READING FROM ALIGNMENT FILE IS ALL REVISED UNTIL f.close()
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itaxotools
parents:
diff changeset
362 line=line.rstrip()
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itaxotools
parents:
diff changeset
363 if line.startswith('>'):
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itaxotools
parents:
diff changeset
364 data = line[1:].split('|')
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itaxotools
parents:
diff changeset
365 if len(data) != 2:
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itaxotools
parents:
diff changeset
366 print('Check number of entries in', data[0])
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itaxotools
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diff changeset
367 #break
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diff changeset
368 data.append('')
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diff changeset
369 imported.append(data)
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itaxotools
parents:
diff changeset
370 else:
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itaxotools
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diff changeset
371 if gaps2D == True:#
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itaxotools
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diff changeset
372 DNA = line.upper().replace('-', 'D').replace('R', 'N').replace('Y', 'N').replace('S','N').replace('W','N').replace('M','N').replace('K','N')#VERYNEW
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diff changeset
373 else:
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itaxotools
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diff changeset
374 DNA = line.upper().replace('-', 'N').replace('R', 'N').replace('Y', 'N').replace('S','N').replace('W','N').replace('M','N').replace('K','N')#VERYNEW
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itaxotools
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diff changeset
375 imported[-1][-1] = imported[-1][-1]+DNA
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itaxotools
parents:
diff changeset
376 f.close()
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diff changeset
377 else:
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diff changeset
378 f = open(ParDict['INPUT_FILE'], 'r')
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itaxotools
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diff changeset
379 for line in f:#VERYNEW - THE DATA READING FROM ALIGNMENT FILE IS ALL REVISED UNTIL f.close()
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diff changeset
380 line=line.rstrip()
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diff changeset
381 data = line.split('\t')
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diff changeset
382 if len(data) != 3:
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diff changeset
383 print('Check number of entries in', data[0])
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diff changeset
384 ID = data[0]
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diff changeset
385 thetax = data[1]
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parents:
diff changeset
386 if gaps2D == True:#
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diff changeset
387 DNA = data[2].upper().replace('-', 'D').replace('R', 'N').replace('Y', 'N').replace('S','N').replace('W','N').replace('M','N').replace('K','N')#VERYNEW
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diff changeset
388 else:
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diff changeset
389 DNA = data[2].upper().replace('-', 'N').replace('R', 'N').replace('Y', 'N').replace('S','N').replace('W','N').replace('M','N').replace('K','N')#VERYNEW
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itaxotools
parents:
diff changeset
390 imported.append([ID, thetax, DNA])
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itaxotools
parents:
diff changeset
391 f.close()
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itaxotools
parents:
diff changeset
392
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diff changeset
393 if 'NumberN' in list(ParDict.keys()):#How many ambiguously called nucleotides are allowed
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parents:
diff changeset
394 NumberN = int(ParDict['NumberN'])
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parents:
diff changeset
395 else:
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diff changeset
396 NumberN = 5
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diff changeset
397
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diff changeset
398 if len(set([len(i[2]) for i in imported])) != 1:
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itaxotools
parents:
diff changeset
399 print('Alignment contains sequences of different lengths:', set([len(i[2]) for i in imported]))
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parents:
diff changeset
400 else:
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diff changeset
401 mlen, sstart, send = medianSeqLen([i[2] for i in imported])#OCT2022 - start
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itaxotools
parents:
diff changeset
402 if mlen + NumberN < len(imported[0][2]):
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diff changeset
403 Slice = True
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diff changeset
404 FragmentLen = mlen
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diff changeset
405 corr = sstart
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diff changeset
406 else:
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diff changeset
407 Slice = False
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diff changeset
408 FragmentLen = len(imported[0][2])
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itaxotools
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diff changeset
409 sstart = 0
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itaxotools
parents:
diff changeset
410 send = FragmentLen+1
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itaxotools
parents:
diff changeset
411 corr = 0
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itaxotools
parents:
diff changeset
412 raw_records=[]
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itaxotools
parents:
diff changeset
413 for i in imported:
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itaxotools
parents:
diff changeset
414 if ParDict['Iref'] != 'NO' and ParDict['Iref'].split(',')[0] == i[0] and ParDict['Iref'].split(',')[1] in ['ex', 'excl', 'out']:
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itaxotools
parents:
diff changeset
415 continue
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diff changeset
416 else:
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parents:
diff changeset
417 if i[2][sstart:send].count('N') < NumberN and len(i[2][sstart:send]) == FragmentLen:
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parents:
diff changeset
418 newi = [i[0], i[1], i[2][sstart:send]]
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itaxotools
parents:
diff changeset
419 raw_records.append(newi)#OCT2022 - end
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itaxotools
parents:
diff changeset
420 print('\n########################## PARAMETERS ######################\n')#VERYNEW
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parents:
diff changeset
421 #print('input file:', ParDict['ORIG_FNAME']) #Outcommented ORIG_FNAME
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parents:
diff changeset
422 print('input file:', ParDict['INPUT_FILE']) #Replacement of the line above
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itaxotools
parents:
diff changeset
423 print('Coding gaps as characters:', gaps2D)
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itaxotools
parents:
diff changeset
424 print('Maximum undetermined nucleotides allowed:', NumberN)
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parents:
diff changeset
425 print('Length of the alignment:', len(imported[0][2]),'->', FragmentLen)
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itaxotools
parents:
diff changeset
426 print('Indexing reference:', ParDict['Iref'].replace('NO', 'Not set').replace('in', 'included').replace('ex', 'excluded'))
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itaxotools
parents:
diff changeset
427 print('Read in', len(raw_records), 'sequences')
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itaxotools
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diff changeset
428
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itaxotools
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diff changeset
429 PosArrays, VarPosList = PositionArrays([i[2] for i in raw_records])#VERYNEW
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itaxotools
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diff changeset
430
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itaxotools
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431 #############################################READ IN OTHER ANALYSIS PARAMETERS
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itaxotools
parents:
diff changeset
432 ##OCT2022 - start
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itaxotools
parents:
diff changeset
433 withplus = []
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itaxotools
parents:
diff changeset
434 P2 = []
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itaxotools
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diff changeset
435 shift = True
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itaxotools
parents:
diff changeset
436 if ParDict['qTAXA'][0] == '>':#THIS OPTION DIAGNOSES ALL TAXA WITH MORE THAN USER-DEFINED NUMBER OF SEQUENCES AVAILABLE
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itaxotools
parents:
diff changeset
437 NumSeq = int(ParDict['qTAXA'][1:])
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parents:
diff changeset
438 Taxarecords = [i[1] for i in raw_records]
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itaxotools
parents:
diff changeset
439 qCLADEs = []
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parents:
diff changeset
440 for j in set(Taxarecords):
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itaxotools
parents:
diff changeset
441 if Taxarecords.count(j) >= NumSeq:
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itaxotools
parents:
diff changeset
442 qCLADEs.append(j)
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itaxotools
parents:
diff changeset
443 elif ParDict['qTAXA'].startswith('P:'):#THIS OPTION DIAGNOSES ALL TAXA CONTAINING A USER-DEFINED PATTERN IN THE NAME
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itaxotools
parents:
diff changeset
444 pattern = ParDict['qTAXA'].split(':')[1]
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itaxotools
parents:
diff changeset
445 Taxarecords = [i[1] for i in raw_records]
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diff changeset
446 qCLADEs = []
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itaxotools
parents:
diff changeset
447 for j in set(Taxarecords):
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itaxotools
parents:
diff changeset
448 if pattern in j:
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diff changeset
449 qCLADEs.append(j)
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itaxotools
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diff changeset
450 elif ParDict['qTAXA'].startswith('P+:'):#THIS OPTION POOLS ALL TAXA CONTAINING A USER-DEFINED PATTERN IN THE NAME IN ONE TAXON AND DIAGNOSES IT
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itaxotools
parents:
diff changeset
451 pattern = ParDict['qTAXA'].split(':')[1]
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itaxotools
parents:
diff changeset
452 Taxarecords = set([i[1] for i in raw_records if pattern in i[1]])
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itaxotools
parents:
diff changeset
453 spp = '+'.join(sorted(list(Taxarecords)))
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itaxotools
parents:
diff changeset
454 qCLADEs = [spp]
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itaxotools
parents:
diff changeset
455 nrecords = []
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parents:
diff changeset
456 for rec in raw_records:
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itaxotools
parents:
diff changeset
457 if rec[1] in Taxarecords:
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itaxotools
parents:
diff changeset
458 nrecords.append([rec[0], spp, rec[2]])
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itaxotools
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diff changeset
459 else:
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parents:
diff changeset
460 nrecords.append(rec)
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itaxotools
parents:
diff changeset
461 raw_records = nrecords
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itaxotools
parents:
diff changeset
462 else:#THIS OPTION DIAGNOSES ALL TAXA FROM A USER-DEFINED LIST; TAXA MAY BE COMBINED BY USING '+'
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itaxotools
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diff changeset
463 qCLADEs = []
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itaxotools
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diff changeset
464 allrecs = ParDict['qTAXA'].split(',')
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parents:
diff changeset
465 for item in allrecs:
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itaxotools
parents:
diff changeset
466 if item in ['ALL', 'All', 'all']:#THIS OPTION DIAGNOSES ALL TAXA IN THE DATASET
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itaxotools
parents:
diff changeset
467 qCLADEs = list(set([i[1] for i in raw_records]))
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itaxotools
parents:
diff changeset
468 elif item in [i[1] for i in raw_records]:
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itaxotools
parents:
diff changeset
469 qCLADEs.append(item)
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diff changeset
470 elif '+' in item:
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diff changeset
471 withplus.append(item)
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diff changeset
472 elif 'VS' in item:
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diff changeset
473 P2.append(item.split('VS'))
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diff changeset
474 else:
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diff changeset
475 print('UNRECOGNIZED TAXON', item)
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diff changeset
476 #OCT2022 - end
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diff changeset
477 print('query taxa:', len(qCLADEs+withplus), '-', str(sorted(qCLADEs)+sorted(withplus)).replace('[','').replace(']','').replace("'", ''))#1.3
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diff changeset
478
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diff changeset
479 if 'Cutoff' in list(ParDict.keys()):#CUTOFF Number of the informative positions to be considered, default 100
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diff changeset
480 Cutoff = ParDict['Cutoff']#VERYNEW
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diff changeset
481 else:
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diff changeset
482 Cutoff = 100
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diff changeset
483 print('Cutoff set as:', Cutoff)
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484 if 'Number_of_iterations' in list(ParDict.keys()):#Number iterations of MolD
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diff changeset
485 N1 = int(ParDict['Number_of_iterations'])
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486 else:
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diff changeset
487 N1 = 10000
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488 print('Number iterations of MolD set as:', N1)
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diff changeset
489
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490 if 'MaxLen1' in list(ParDict.keys()):#Maximum length for the raw mDNCs
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491 MaxLen1 = int(ParDict['MaxLen1'])
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492 else:
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493 MaxLen1 = 12
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494 print('Maximum length of raw mDNCs set as:', MaxLen1)
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diff changeset
495
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496 if 'MaxLen2' in list(ParDict.keys()):#Maximum length for the refined mDNCs
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497 MaxLen2 = int(ParDict['MaxLen2'])
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498 else:
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499 MaxLen2 = 7
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500 print('Maximum length of refined mDNCs set as:', MaxLen2)
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diff changeset
501
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diff changeset
502 if 'Pdiff' in list(ParDict.keys()):#Percent difference
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503 Percent_difference = float(ParDict['Pdiff'])
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504 else:
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diff changeset
505 if int(ParDict['Taxon_rank']) == 1:#read in taxon rank to configure Pdiff parameter of artificial dataset
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diff changeset
506 Percent_difference = 1
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507 else:
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508 Percent_difference = 5
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509 print('simulated sequences up to', Percent_difference, 'percent divergent from original ones')
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parents:
diff changeset
510
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diff changeset
511 if 'NMaxSeq' in list(ParDict.keys()):#Maximum number of sequences per taxon to be modified
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diff changeset
512 Seq_per_clade_to_screw = int(ParDict['NMaxSeq'])
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513 else:
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diff changeset
514 Seq_per_clade_to_screw = 10####!changed value
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parents:
diff changeset
515 print('Maximum number of sequences modified per clade', Seq_per_clade_to_screw)
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diff changeset
516
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diff changeset
517 if 'Scoring' in list(ParDict.keys()):
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518 if ParDict['Scoring'] == 'lousy':
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diff changeset
519 threshold = 66####!changed value
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diff changeset
520 elif ParDict['Scoring'] == 'moderate':
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diff changeset
521 threshold = 75####!changed value
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522 elif ParDict['Scoring'] == 'stringent':
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523 threshold = 90####!changed value
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diff changeset
524 elif ParDict['Scoring'] == 'very_stringent':
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diff changeset
525 threshold = 95####!changed value
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526 else:
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diff changeset
527 threshold = 75####!changed value
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diff changeset
528 else:
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diff changeset
529 threshold = 75####!changed value
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530 #print(ParDict['Scoring'], 'scoring of the rDNCs; threshold in two consequtive runs:', threshold)
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diff changeset
531 print('scoring of the rDNCs; threshold in two consequtive runs:', threshold)
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itaxotools
parents:
diff changeset
532 #OCT2022 - start
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itaxotools
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diff changeset
533 if corr > 1 and len(ParDict['Iref'].split(',')) == 2:
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diff changeset
534 print('\nNOTE: The alignment was trimmed automatically to match median sequences length. The analysed slice starts from the site',str(sstart+1),'and ends on the site',str(send+1),'. The site indexing in the DNCs as in the provided reference.')
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diff changeset
535 if corr > 1 and ParDict['Iref'] == 'NO':
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itaxotools
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diff changeset
536 print('\nNOTE: The alignment was trimmed automatically to match median sequences length. The analysed slice starts from the site',str(sstart+1),'and ends on the site',str(send+1),'. The site indexing in the rDNC as in the untrimmed alignment.')
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itaxotools
parents:
diff changeset
537 #OCT2022 - end
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diff changeset
538 thephrase = 'The DNA diagnosis for the taxon'
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itaxotools
parents:
diff changeset
539 ###################################################IMPLEMENTATION
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itaxotools
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diff changeset
540 #Setting up a new class just for the convenient output formatting
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diff changeset
541 class SortedDisplayDict(dict):#this is only to get a likable formatting of the barcode
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diff changeset
542 def __str__(self):
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diff changeset
543 return "[" + ", ".join("%r: %r" % (key, self[key]) for key in sorted(self)) + "]"
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itaxotools
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diff changeset
544
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itaxotools
parents:
diff changeset
545 class SortedDisplayDictVerbose(dict):#this is only to get a likable formatting of the barcode
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parents:
diff changeset
546 def __str__(self):
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diff changeset
547 return ", ".join("%r %r" % (self[key],'in the site '+str(key)) for key in sorted(self)).replace("'", '').replace("A", "'A'").replace("C", "'C'").replace("G", "'G'").replace("T", "'T'")+'.'
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itaxotools
parents:
diff changeset
548
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itaxotools
parents:
diff changeset
549 #Calling functions and outputing results
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parents:
diff changeset
550 if ParDict['OUTPUT_FILE'] == "str":
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diff changeset
551 g = StringIO()
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diff changeset
552 else:
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parents:
diff changeset
553 g = open(ParDict['OUTPUT_FILE'], "w")#Initiating output file
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itaxotools
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diff changeset
554 #VERYNEW
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diff changeset
555 print('<h4>########################## PARAMETERS ######################</h4>', file=g)
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itaxotools
parents:
diff changeset
556 #print("<p>", 'input file:', ParDict['ORIG_FNAME'], "</p>", file=g) #outcommented ORIG_FNAME
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diff changeset
557 print("<p>", 'input file:', ParDict['INPUT_FILE'], "</p>", file=g)
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parents:
diff changeset
558 print("<p>", 'Coding gaps as characters:', gaps2D, "</p>", file=g)
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itaxotools
parents:
diff changeset
559 print("<p>", 'Maximum undetermined nucleotides allowed:', NumberN, "</p>", file=g)
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itaxotools
parents:
diff changeset
560 print("<p>", 'Length of the alignment:', len(imported[0][2]),'->', FragmentLen, "</p>", file=g)
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itaxotools
parents:
diff changeset
561 print("<p>", 'Indexing reference:', ParDict['Iref'].replace('NO', 'Not set').replace('in', 'included').replace('ex', 'excluded'), "</p>", file=g)#OCT2022
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parents:
diff changeset
562 print("<p>", 'Read in', len(raw_records), 'sequences', "</p>", file=g)
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itaxotools
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diff changeset
563 print("<p>", 'query taxa:', len(qCLADEs+withplus), '-', str(sorted(qCLADEs)+sorted(withplus)).replace('[','').replace(']','').replace("'", ''), "</p>", file=g)#1.3
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itaxotools
parents:
diff changeset
564 print("<p>", 'Cutoff set as:', Cutoff, "</p>", file=g)
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parents:
diff changeset
565 print("<p>", 'Number iterations of MolD set as:', N1, "</p>", file=g)
4e8e2f836d0f planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
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parents:
diff changeset
566 print("<p>", 'Maximum length of raw mDNCs set as:', MaxLen1, "</p>", file=g)
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itaxotools
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diff changeset
567 print("<p>", 'Maximum length of refined mDNCs set as:', MaxLen2, "</p>", file=g)
4e8e2f836d0f planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
568 print("<p>", 'simulated sequences up to', Percent_difference, 'percent divergent from original ones', "</p>", file=g)
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parents:
diff changeset
569 print("<p>", 'Maximum number of sequences modified per clade', Seq_per_clade_to_screw, "</p>", file=g)
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parents:
diff changeset
570 #print("<p>", ParDict['Scoring'], 'scoring of the rDNCs; threshold in two consequtive runs:', threshold, "</p>", file=g)
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itaxotools
parents:
diff changeset
571 print("<p>", 'scoring of the rDNCs; threshold in two consequtive runs:', threshold, "</p>", file=g)
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itaxotools
parents:
diff changeset
572 if corr > 1 and len(ParDict['Iref'].split(',')) == 2:
4e8e2f836d0f planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
573 print('<h4>NOTE: The alignment was trimmed automatically to match median sequences length. The analysed slice starts from the site',str(sstart+1),'and ends on the site',str(send+1),'. The site indexing in the DNCs as in the provided reference.</h4>', file=g)
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itaxotools
parents:
diff changeset
574 if corr > 1 and ParDict['Iref'] == 'NO':
4e8e2f836d0f planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
575 print('<h4>NOTE: The alignment was trimmed automatically to match median sequences length. The analysed slice starts from the site',str(sstart+1),'and ends on the site',str(send+1),'. The site indexing in the rDNC as in the untrimmed alignment.</h4>', file=g)
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diff changeset
576
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parents:
diff changeset
577 print('<h4>########################### RESULTS ##########################</h4>', file=g)
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itaxotools
parents:
diff changeset
578
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parents:
diff changeset
579 for qCLADE in sorted(qCLADEs) + sorted(withplus):#OCT2022
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itaxotools
parents:
diff changeset
580 if '+' in qCLADE:
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itaxotools
parents:
diff changeset
581 if shift == True:
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itaxotools
parents:
diff changeset
582 old_records = raw_records
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itaxotools
parents:
diff changeset
583 shift == False
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itaxotools
parents:
diff changeset
584 else:
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itaxotools
parents:
diff changeset
585 raw_records = old_records
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itaxotools
parents:
diff changeset
586 spp = qCLADE.split('+')
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parents:
diff changeset
587 nrecords = []
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parents:
diff changeset
588 for rec in raw_records:
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parents:
diff changeset
589 if rec[1] in spp:
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parents:
diff changeset
590 nrecords.append([rec[0], qCLADE, rec[2]])
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itaxotools
parents:
diff changeset
591 else:
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itaxotools
parents:
diff changeset
592 nrecords.append(rec)
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itaxotools
parents:
diff changeset
593 raw_records = nrecords
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itaxotools
parents:
diff changeset
594 print('\n**************', qCLADE, '**************')
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itaxotools
parents:
diff changeset
595 print('<h4>**************', qCLADE, '**************</h4>', file=g)
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parents:
diff changeset
596 Clades, clade_sorted_seqs, shared_positions = Step1(raw_records)#STEP1
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itaxotools
parents:
diff changeset
597 x,y,z,pures = C_VP_PP(clade_sorted_seqs, qCLADE, shared_positions, Cutoff)#STEP2 ####! added pures
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parents:
diff changeset
598 newy = {key:y[key] for key in y if not key in pures} ####! newline
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itaxotools
parents:
diff changeset
599 print('Sequences analyzed:', len(clade_sorted_seqs[qCLADE]))
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parents:
diff changeset
600 print("<p>",'Sequences analyzed:', len(clade_sorted_seqs[qCLADE]), "</p>", file=g)
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itaxotools
parents:
diff changeset
601 ND_combinations = [[item] for item in pures] ####! before ND_combinations were initiated as an empty list
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itaxotools
parents:
diff changeset
602 print('single nucleotide mDNCs:', len(pures), '-', str(SortedDisplayDict({pos+corr : y[pos-1] for pos in [i+1 for i in pures]}))[1:-1])#OCT2022
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itaxotools
parents:
diff changeset
603 print("<p>",'single nucleotide mDNCs*:',len(pures), '-', str(SortedDisplayDict({pos+corr : y[pos-1] for pos in [i+1 for i in pures]}))[1:-1], "</p>", file=g)#OCT2022
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itaxotools
parents:
diff changeset
604 N = 1 ####!
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itaxotools
parents:
diff changeset
605 while N > 0:#STEP3
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parents:
diff changeset
606 try:
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parents:
diff changeset
607 q = Diagnostic_combinations(qCLADE, x, newy, N1, MaxLen1, MaxLen2) ####! newy instead of y
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itaxotools
parents:
diff changeset
608 except IndexError:
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itaxotools
parents:
diff changeset
609 print(N, 'IndexError')
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itaxotools
parents:
diff changeset
610 continue
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itaxotools
parents:
diff changeset
611 for comb in q:
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itaxotools
parents:
diff changeset
612 if not comb in ND_combinations:
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itaxotools
parents:
diff changeset
613 ND_combinations.append(comb)
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itaxotools
parents:
diff changeset
614 N-=1
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parents:
diff changeset
615 ND_combinations.sort(key=len)
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itaxotools
parents:
diff changeset
616 #################################### mDNC output
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itaxotools
parents:
diff changeset
617 try:
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parents:
diff changeset
618 Nind, KeyPos = IndependentKey(ND_combinations)#STEP4
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itaxotools
parents:
diff changeset
619 except IndexError:
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parents:
diff changeset
620 print('no mDNCs recovered for', qCLADE)#VERYNEW
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itaxotools
parents:
diff changeset
621 print("<p>", 'no mDNCs recovered for', "</p>", qCLADE, file=g)#VERYNEW
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itaxotools
parents:
diff changeset
622 continue
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itaxotools
parents:
diff changeset
623 Allpos = []#Create list of all positions involved in mDNCs
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itaxotools
parents:
diff changeset
624 for comb in ND_combinations:
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itaxotools
parents:
diff changeset
625 for pos in comb:
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itaxotools
parents:
diff changeset
626 if not pos in Allpos:
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itaxotools
parents:
diff changeset
627 Allpos.append(pos)
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itaxotools
parents:
diff changeset
628 print('\nmDNCs retrieved:', str(len(ND_combinations)) + '; Sites involved:', str(len(Allpos)) + '; Independent mDNCs:', len(Nind))#VERYNEW
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itaxotools
parents:
diff changeset
629 print("<p>", 'mDNCs* retrieved:', str(len(ND_combinations)) + '; Sites involved:', str(len(Allpos)) + '; Independent mDNCs**:', len(Nind), "</p>", file=g)#VERYNEW
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itaxotools
parents:
diff changeset
630 print('Shortest retrieved mDNC:', SortedDisplayDict({pos+corr : y[pos-1] for pos in [i+1 for i in ND_combinations[0]]}), '\n')#OCT2022
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itaxotools
parents:
diff changeset
631 print("<p>",'Shortest retrieved mDNC*:', SortedDisplayDict({pos+corr : y[pos-1] for pos in [i+1 for i in ND_combinations[0]]}), "</p>", file=g)#OCT2022
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itaxotools
parents:
diff changeset
632 ######################################################## rDNC output
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itaxotools
parents:
diff changeset
633 Barcode_scores = []#Initiate a list for rDNC scores
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itaxotools
parents:
diff changeset
634 npos = len(ND_combinations[0])
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itaxotools
parents:
diff changeset
635 BestBarcode = 'none'####! newline
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itaxotools
parents:
diff changeset
636 while npos <= min([10, len(Allpos)]):#in this loop the positions are added one-by-one to a rDNC and the rDNC is then rated on the artificially generated datasets
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itaxotools
parents:
diff changeset
637 Barcode = GenerateBarcode_new(ND_combinations, npos)#Initiate a rDNC
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itaxotools
parents:
diff changeset
638 Barcode_score = 0#Initiate a score to rate a rDNC
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itaxotools
parents:
diff changeset
639 N = 100
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parents:
diff changeset
640 while N > 0:
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itaxotools
parents:
diff changeset
641 NComplist, NCPP = Screwed_dataset_new(raw_records, Seq_per_clade_to_screw, PosArrays, VarPosList, Percent_difference, qCLADE, Cutoff)#Create an artificial dataset VERYNEW
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itaxotools
parents:
diff changeset
642 NBarcode = [i for i in Barcode if i in list(NCPP.keys())]
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itaxotools
parents:
diff changeset
643 if len(Barcode) - len(NBarcode) <= 1 and ConditionD(NBarcode, NComplist, NCPP) == True:####! new condition (first) added
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itaxotools
parents:
diff changeset
644 Barcode_score +=1
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itaxotools
parents:
diff changeset
645 N -=1
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itaxotools
parents:
diff changeset
646 print(npos, 'rDNC_score (100):', [k+corr+1 for k in Barcode], '-', Barcode_score)#VERYNEW
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itaxotools
parents:
diff changeset
647 print("<p>", npos, 'rDNC_score (100):', [k+corr+1 for k in Barcode], '-', Barcode_score, "</p>", file=g)#OCT2022
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itaxotools
parents:
diff changeset
648 if Barcode_score >= threshold and len(Barcode_scores) == 1: ###1.3
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itaxotools
parents:
diff changeset
649 BestBarcode = Barcode###1.3
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itaxotools
parents:
diff changeset
650 if Barcode_score >= threshold and len(Barcode_scores) > 1 and Barcode_score >= max(Barcode_scores): ###1.3
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itaxotools
parents:
diff changeset
651 BestBarcode = Barcode####!newline
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itaxotools
parents:
diff changeset
652 Barcode_scores.append(Barcode_score)
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itaxotools
parents:
diff changeset
653 if len(Barcode_scores) >= 2 and Barcode_scores[-1] >= threshold and Barcode_scores[-2] >= threshold:#Check whether the rDNC fulfills robustnes criteria 85:85:85
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itaxotools
parents:
diff changeset
654 print('Final rDNC:', SortedDisplayDict({pos+corr : y[pos-1] for pos in [i+1 for i in BestBarcode]}))#OCT2022
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itaxotools
parents:
diff changeset
655 print("<p>",'Final rDNC***:', SortedDisplayDict({pos+corr : y[pos-1] for pos in [i+1 for i in BestBarcode]}), "</p>", file=g)#OCT2022
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itaxotools
parents:
diff changeset
656 print('\n',thephrase, qCLADE, 'is:', SortedDisplayDictVerbose({pos+corr : y[pos-1] for pos in [i+1 for i in BestBarcode]}))#OCT2022
4e8e2f836d0f planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
657 print("<p>", thephrase, qCLADE, 'is:', SortedDisplayDictVerbose({pos+corr : y[pos-1] for pos in [i+1 for i in BestBarcode]}), "</p>", file=g)#OCT2022
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itaxotools
parents:
diff changeset
658 break
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itaxotools
parents:
diff changeset
659 else:# VERY NEW FROM HERE ONWARDS
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itaxotools
parents:
diff changeset
660 npos += 1
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itaxotools
parents:
diff changeset
661 if npos > min([10, len(Allpos)]):
4e8e2f836d0f planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
662 if BestBarcode != 'none':
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itaxotools
parents:
diff changeset
663 print('The highest scoring rDNC for taxon', qCLADE, 'is:', SortedDisplayDictVerbose({pos+corr : y[pos-1] for pos in [i+1 for i in BestBarcode]}))#OCT2022
4e8e2f836d0f planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
664 print("<p>", 'The highest scoring rDNC*** for taxon', qCLADE, 'is:', SortedDisplayDictVerbose({pos+corr : y[pos-1] for pos in [i+1 for i in BestBarcode]}), "</p>", file=g)#OCT2022
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itaxotools
parents:
diff changeset
665 else:
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itaxotools
parents:
diff changeset
666 print('No sufficiently robust DNA diagnosis for taxon', qCLADE, 'was retrieved')
4e8e2f836d0f planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
667 print("<p>", 'No sufficiently robust DNA diagnosis for taxon', qCLADE, 'was retrieved', "</p>", file=g)
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itaxotools
parents:
diff changeset
668 #OCT2022 - start
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itaxotools
parents:
diff changeset
669 print("<h4>", '################################# EXPLANATIONS ####################################', "</h4>", file=g)
4e8e2f836d0f planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
670 print("<p>", ' * mDNC -(=minimal Diagnostic nucleotide combination) is a combination of nucleotides at specified sites of the alignment,', "</p>", file=g)
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itaxotools
parents:
diff changeset
671 print("<p>", ' unique for a query taxon. Therefore it is sufficient to differentiate a query taxon from all reference taxa in a dataset.', "</p>", file=g)
4e8e2f836d0f planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
672 print("<p>", ' Because it comprises minimal necessary number of nucleotide sites to differentiate a query, any mutation in the mDNC in' "</p>", file=g)
4e8e2f836d0f planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
673 print("<p>", ' single specimen of a query taxon will automatically disqualify it as a diagnostic combination.', "</p>", file=g)
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itaxotools
parents:
diff changeset
674 print("<p>", "</p>", file=g)
4e8e2f836d0f planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
675 print("<p>", ' ** two or more mDNCs are INDEPENDENT if they constitute non-overlapping sets of nucleotide sites.', "</p>", file=g)
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itaxotools
parents:
diff changeset
676 print("<p>", "</p>", file=g)
4e8e2f836d0f planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
677 print("<p>", '*** rDNC -(=robust/redundant Diagnostic nucleotide combination) is a combination of nucleotides at specified sites of the alignment,', "</p>", file=g)
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itaxotools
parents:
diff changeset
678 print("<p>", ' unique for a query taxon and (likewise mDNC) sufficient to differentiate a query taxon from all reference taxa in a dataset.', "</p>", file=g)
4e8e2f836d0f planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
679 print("<p>", ' However, rDNC comprises more than a minimal necessary number of diagnostic sites, and therefore is robust to single nucleotide', "</p>", file=g)
4e8e2f836d0f planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
680 print("<p>", ' replacements. Even if a mutation arises in one of the rDNC sites, the remaining ones will (with high probability) remain sufficient ', "</p>", file=g)
4e8e2f836d0f planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
681 print("<p>", ' to diagnose the query taxon', "</p>", file=g)
4e8e2f836d0f planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
682 print("<h4>", ' Final diagnosis corresponds to rDNC', "</h4>", file=g)
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683 #OCT2022 - end
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684
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685 if ParDict['OUTPUT_FILE'] == "str":
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686 contents = g.getvalue()
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687 os.unlink(ParDict['INPUT_FILE'])
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688 else:
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689 contents = None
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690 g.close()
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691 #OCT2022 - start
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692 if len(P2) != 0:
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693 ext = '.'+ParDict['OUTPUT_FILE'].split('.')[-1]
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694 h = open(ParDict['OUTPUT_FILE'].replace(ext, '_pairwise'+ext), "w")#Initiating output file
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695 if len(withplus) != 0:
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696 raw_records = old_records
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697 taxain = [i[1] for i in raw_records]
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698 tpairs = []
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699 for alist in P2:
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700 if alist.count('all')+alist.count('All')+alist.count('ALL') == 2:
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701 tpairs = getAllPairs(taxain)
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702 elif alist.count('all')+alist.count('All')+alist.count('ALL') == 1:
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703 thetax = [i for i in taxain if i in alist][0]
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704 print(thetax)
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705 for atax in sorted(list(set(taxain))):
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706 if atax != thetax:
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707 tpairs.append([thetax, atax])
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708 else:
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709 for apair in getAllPairs(alist):
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710 tpairs.append(apair)
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711 for apair in tpairs:
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712 t1 = apair[0]
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713 t2 = apair[1]
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714 p2records = [i for i in raw_records if i[1] in [t1, t2]]
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715 print('\n**************', t1, 'VS', t2,'**************')
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716 print('<h4>**************', t1, 'VS', t2, '**************</h4>', file=h)
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717 C2, css2, sp2 = Step1(p2records)#STEP1
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718 x2,y2,z2,pures2 = C_VP_PP(css2, t1, sp2, '>0')#STEP2 ####! added pures
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719 Pairphrase = 'Each of the following '+ str(len(pures2))+' sites is invariant across sequences of '+ t1+ ' and differentiates it from '+ t2+': '
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720 counterPures = {}
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721 for site in pures2:
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722 counterPures[site] = "'or'".join(list(set([thing[site] for thing in css2[t2] if thing[site] != 'N'])))
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723 Pairphrase = Pairphrase + str(site+corr)+" ('"+str(y2[site])+"' vs '"+str(counterPures[site])+"'), "
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parents:
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724 print(Pairphrase[:-2])
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725 print("<p>",Pairphrase[:-2],'</h4>', file=h)#OCT2022
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726 x2r,y2r,z2r,pures2r = C_VP_PP(css2, t2, sp2, '>0')#STEP2 ####! added pures
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727 Pairphraser = 'Each of the following '+ str(len(pures2r))+' sites is invariant across sequences of '+ t2+ ' and differentiates it from '+ t1+': '
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728 counterPuresr = {}
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729 for site in pures2r:
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diff changeset
730 counterPuresr[site] = "'or'".join(list(set([thing[site] for thing in css2[t1] if thing[site] != 'N'])))
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731 Pairphraser = Pairphraser + str(site+corr)+" ('"+str(y2r[site])+"' vs '"+str(counterPuresr[site])+"'), "
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732 print(Pairphraser[:-2])
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733 print("<p>",Pairphraser[:-2],'</h4>', file=h)#OCT2022
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734 h.close()
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735
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736 #OCT2022 - end
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itaxotools
parents:
diff changeset
737 return contents, qCLADEs
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itaxotools
parents:
diff changeset
738 if __name__ == "__main__":
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739 c, q = mainprocessing()
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740