Mercurial > repos > abims-sbr > pogs

annotate scripts/pogs.py @ 6:b19ed7395dcc draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
author abims-sbr
date Wed, 17 Jan 2018 08:54:30 -0500
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children 1a728cb1da31
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1 #!/usr/bin/env python
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2 # coding: utf8
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3 # September 2017 - Author : Victor Mataigne (Station Biologique de Roscoff - ABiMS)
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4 # Command line : ./pogsPOO.py <list_of_input_files_separated_by_commas> <minimal number of species per group> [-v) [-p]
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6 """
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7 What it does:
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8 - pogs.py parses output files from the "pairwise" tool of the AdaptSearch suite and proceeds to gather genes in orthogroups (using transitivity).
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9 - A minimal number of species per group has to be set.
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11 BETA VERSION
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12 """
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14 import os, argparse
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15 import numpy as np
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16 import pandas as pd
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18 """ Definition of a locus : header + sequence + a tag """
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19 class Locus:
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21 def __init__(self, header, sequence):
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22 self.header = header
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23 self.sequence = sequence
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24 self.tagged = False
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26 def __str__(self):
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27 return "{}{}".format(self.header, self.sequence)
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29 def __eq__(self, other):
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30 return self.getHeader() == other.getHeader() # Test if two loci are the same
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32 def __hash__(self):
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33 return hash((self.header, self.sequence)) # Make the object iterable and hashable
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35 def getHeader(self):
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36 return self.header
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38 def getSequence(self):
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39 return self.sequence
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41 def getTag(self):
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42 return self.tagged
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44 def prettyPrint(self):
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45 # Used for debugging : print "{ Header : ", self.header[0:-1], "Tag : ", self.tagged, " }"
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46 print "[ Header : {header} ]".format(header=self.header[0:-1])
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47
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48 def prettyPrint2(self):
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49 print "[ Header : {header} Sequence : {sequence} ]".format(header=self.header[0:-1], sequence=self.sequence[0:-1])
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51 """ Applies the getPairwiseCouple() function to a list of files and return a big list with ALL pairwises couples
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52 Returns a list of sets (2 items per set) """
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53 def getListPairwiseAll(listPairwiseFiles):
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55 # Sub-Function
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56
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57 """ Reads an output file from the 'Pairwise' tool (AdaptSearch suite) and returns its content into a list
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58 Returns a list of sets (2 items per set) """
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59 def getPairwiseCouple(pairwiseFile):
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60 list_pairwises_2sp = []
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61 with open(pairwiseFile, "r") as file:
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62 while (1): # Ugly !
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63 name, sequence, name2, sequence2 = file.readline(), file.readline(), file.readline(), file.readline()
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64 if not name: break # Use assert ?
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65 # One locus every two lines (one pairwise couple = 4 lines) : header + sequence
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66 locus1 = Locus(name, sequence)
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67 locus2 = Locus(name2, sequence2)
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68 group = set([])
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69 group.add(locus1)
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70 group.add(locus2)
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71 list_pairwises_2sp.append(group)
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72 return (list_pairwises_2sp)
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74 # Function
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75 list_pairwises_allsp = []
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76 for file in listPairwiseFiles:
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77 listPairwises = getPairwiseCouple(file)
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78 for pairwise in listPairwises:
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79 list_pairwises_allsp.append(pairwise) # all pairwises in the same 1D list
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80 return list_pairwises_allsp
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81
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82 """ Proceeds to create orthogroups by putting together pairwise couples sharing a locus.
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83 Iterates over the orthogroups list and tag to 'True' the pairwise couple already gathered in a group to avoid
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84 redondancy. Writes each orthogroup in a fasta file
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85 Returns an integer (a list length) """
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86 def makeOrthogroups(list_pairwises_allsp, minspec, nb_rbh, verbose, paralogs):
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87
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88 # Sub-funtions
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89
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90 """ Check if a locus/group has already been treated in makeOrthogroups()
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91 Returns a boolean """
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92 def checkIfTagged(pair):
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93 tag = True
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94 for element in pair:
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95 if not element.getTag() and tag: # use a list comprehension maybe ?
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96 tag = False
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97 return tag
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98
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99 """ True means a locus/group has already been treated in makeOrthogroups()
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100 A stronger code would be to implement a method inside the class Locus """
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101 def tagGroup(pair):
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102 for element in pair:
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103 element.tagged = True
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104
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105 """ Write an orthogroup in a file """
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106 def writeOutputFile(orthogroup, number, naming):
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107 name = ""
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108 if naming:
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109 name = "orthogroup_{}_with_{}_sequences_withParalogs.fasta".format(number, len(orthogroup))
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110 else :
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111 name = "orthogroup_{}_with_{}_sequences.fasta".format(number, len(orthogroup))
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112 result = open(name, "w")
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113 with result:
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114 for locus in orthogroup:
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115 if locus.getHeader()[-1] == "\n":
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116 result.write("%s" % locus.getHeader()) # write geneID
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117 else :
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118 result.write("%s\n" % locus.Header()) # write geneID
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119 if locus.getSequence()[-1] == "\n":
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120 result.write("%s" % locus.getSequence()) # write sequence
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121 else :
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122 result.write("%s\n" % locus.getSequence()) # write sequence
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123 if naming:
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124 os.system("mv {} outputs_withParalogs/".format(name))
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125 else :
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126 os.system("mv {} outputs/".format(name))
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127
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128 """ Parse an orthogroup list to keep only one paralog sequence per species & per group
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129 (Keeps the 1st paralogous encoutered)
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130 Returns a list """
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131 def filterParalogs(list_orthogroups, minspec):
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132 list_orthogroups_format = []
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133 j = 1
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134
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135 for nofilter_group in list_orthogroups:
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136 new_group = []
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137 species = {}
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138 for loci in nofilter_group:
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139 species[loci.getHeader()[1:3]] = False
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140 for loci in nofilter_group:
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141 if not species[loci.getHeader()[1:3]]:
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142 new_group.append(loci)
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143 species[loci.getHeader()[1:3]] = True
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144
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145 if len(new_group) >= minspec: # Drop too small orthogroups
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146 list_orthogroups_format.append(new_group)
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147 writeOutputFile(new_group, j, False)
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148 j += 1
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149
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150 return list_orthogroups_format
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151
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152 """ Builds a 2D array for a summary
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153 Returns a numpy 2D array """
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154 def countings(listOrthogroups, nb_rbh):
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155
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156 def compute_nbspec(nb_rbh):
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157
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158 def factorielle(x):
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159 n = 1
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160 s = 0
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161 while n <= x:
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162 s += n
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163 n += 1
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164 return s
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165
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166 x = 2
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167 nb_specs = 0
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168 while x*x - factorielle(x) < nb_rbh:
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169 x += 1
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170 return x
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171 #listOrthogroups.sort().reverse()
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172 #nblines = len(listOrthogroups[0])
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173 nblines = 0
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174 for group in listOrthogroups:
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175 if len(group) > nblines:
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176 nblines = len(group)
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177 matrix = np.array([[0]*compute_nbspec(nb_rbh)]*nblines)
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178
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179 for group in listOrthogroups:
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180 listSpecs = []
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181 for loci in group:
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182 if loci.getHeader()[1:3] not in listSpecs:
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183 listSpecs.append(loci.getHeader()[1:3])
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184 matrix[len(group)-1][len(listSpecs)-1] += 1
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185
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186 return matrix
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187
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188 """ numpy 2D array in a nice dataframe
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189 Returns a pandas 2D dataframe """
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190 def asFrame(matrix) :
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191 index = [0]*len(matrix)
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192 colnames = [0]*len(matrix[0])
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193 index = [str(i+1)+" seqs" for i in range(len(matrix))]
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194 colnames = [str(i+1)+" sps" for i in range(len(matrix[0]))]
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195 df = pd.DataFrame(matrix, index=index, columns=colnames)
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196 return df # Mettre une selection pour ne renvoyer que les lignes et les colonnes qui somment > 0
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197 #return df.loc['4 seqs':'9 seqs'].loc[:,colnames[3:]]
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198
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199 # Function -------------------------------------------------------------------------------------------------
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200 list_orthogroups = []
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201
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202 for ortho_pair1 in list_pairwises_allsp[0:-1]:
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203 if not checkIfTagged(ortho_pair1):
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204 orthogroup = ortho_pair1 # the orthogroup grows as we go throught the second loop
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205
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206 # check for common locus between two groups
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207 for ortho_pair2 in list_pairwises_allsp[list_pairwises_allsp.index(ortho_pair1) + 1:]:
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208 if len(orthogroup.intersection(ortho_pair2)) != 0 and not checkIfTagged(ortho_pair2):
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209 orthogroup.update(orthogroup | ortho_pair2)
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210 tagGroup(ortho_pair2)
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211
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212 # Check if subgroup is already computed
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213 if len(list_orthogroups) > 0:
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214 presence = False
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215 for group in list_orthogroups:
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216 if len(group.intersection(orthogroup)) != 0:
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217 group.update(group | orthogroup)
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218 presence = True
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219 if not presence:
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220 list_orthogroups.append(orthogroup)
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221 else:
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222 list_orthogroups.append(orthogroup)
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223
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224 # Options --------------------------------------------------------------------------------------------------
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225
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226 """ nb : I could try to implement a more complex code which does in the same previous loop all the following lines, to avoid multiples parsing of
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227 the orthogroups list, but the code would become hardly readable. Since the whole program is already quite fast, I chosed code simplicity
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228 over code efficiency """
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229
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230 # Print summary table with all paralogs
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231 if verbose :
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232 frame = countings(list_orthogroups, nb_rbh)
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233 df = asFrame(frame)
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234 print "\n Summary before paralogous filtering : \n"
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235 print df.loc[df.ne(0).any(1),df.ne(0).any()], "\n" # Don't display columns and lines filled with 0
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236
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237 # Write outputFile with all the paralogous
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238 if paralogs:
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239 print "Writing orthogroups with paralogs files ...\n"
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240 j = 1
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241 for group in list_orthogroups:
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242 if len(group) >= minspec:
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243 writeOutputFile(group, j, True)
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244 j += 1
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245
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246 # Paralogs filtering and summary ----------------------------------------------------------------------------
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247
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248 print "Filtering paralogous sequences and writing final orthogroups files ..."
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249 print " (Dropping Orthogroups with less than {} species)".format(minspec)
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250
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251 # writeOutputFile() is called in filterParalogs()
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252 list_orthogroups_format = filterParalogs(list_orthogroups, minspec)
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253
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254 frame = countings(list_orthogroups_format, nb_rbh)
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255 df = asFrame(frame)
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256 print "\n Summary after paralogous filtering : \n"
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257 print df.loc[df.ne(0).any(1),df.ne(0).any()]
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258
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259 #return only the length of the list (at this point the program doesn't need more)
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260 return len(list_orthogroups_format)
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261
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262 def main():
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263 parser = argparse.ArgumentParser()
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264 parser.add_argument("files", help="Input files separated by commas. Each file contains all the reciprocical best hits between a pair of species")
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265 parser.add_argument("minspec", help="Only keep Orthogroups with at least this number of species", type=int)
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266 parser.add_argument("-v", "--verbose", action="store_true", help="A supplemental summary table of orthogroups before paralogs filtering will be returned")
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267 parser.add_argument("-p", "--paralogs", action="store_true", help="Proceeds to write orthogroups also before paralogous filtering")
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268 args = parser.parse_args()
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269
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270 print "*** pogs.py ***"
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271 print "\nBuilding of orthogroups based on pairs of genes obtained by pairwise comparisons between pairs of species."
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272 print "Genes are gathered in orthogroups based on the principle of transitivity between genes pairs."
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273
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274 os.system("mkdir outputs")
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275 if args.paralogs: os.system("mkdir outputs_withParalogs")
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276 infiles = args.files
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277 listPairwiseFiles = str.split(infiles, ",")
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278 print "\nParsing input files ..."
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279 list_Locus = getListPairwiseAll(listPairwiseFiles)
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280 print "Creating Orthogroups ..."
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281 nb_orthogroups = makeOrthogroups(list_Locus, args.minspec, len(listPairwiseFiles), args.verbose, args.paralogs)
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282 print "\n{} orthogroups have been infered from {} pairwise comparisons by RBH\n".format(nb_orthogroups, len(listPairwiseFiles))
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283
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284 if __name__ == "__main__":
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285 main()