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1 #!/usr/bin/env python
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2 #####################################################################################
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3 #Copyright (C) <2012>
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4 #
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5 #Permission is hereby granted, free of charge, to any person obtaining a copy of
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6 #this software and associated documentation files (the "Software"), to deal in the
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7 #Software without restriction, including without limitation the rights to use, copy,
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8 #modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
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9 #and to permit persons to whom the Software is furnished to do so, subject to
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10 #the following conditions:
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11 #
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12 #The above copyright notice and this permission notice shall be included in all copies
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13 #or substantial portions of the Software.
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14 #
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15 #THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
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16 #INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
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17 #PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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18 #HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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19 #OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
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20 #SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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21 #
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22 # This file is a component of the MaAsLin (Multivariate Associations Using Linear Models),
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23 # authored by the Huttenhower lab at the Harvard School of Public Health
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24 # (contact Timothy Tickle, ttickle@hsph.harvard.edu).
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25 #####################################################################################
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26
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27 __author__ = "Timothy Tickle"
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28 __copyright__ = "Copyright 2012"
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29 __credits__ = ["Timothy Tickle"]
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30 __license__ = ""
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31 __version__ = ""
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32 __maintainer__ = "Timothy Tickle"
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33 __email__ = "ttickle@sph.harvard.edu"
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34 __status__ = "Development"
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35
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36 import argparse
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37 import csv
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38 from operator import itemgetter
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39 import re
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40 import sys
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41
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42 #Helper function which returns a boolean indicator of an input string being parsable as an int
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43 def funcIsInt(strInt):
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44 try:
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45 int(strInt)
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46 return True
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47 except:
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48 return False
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49
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50 #Helper function that gets the index of the name and gives the last value of the list for - or the first value depending on the position
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51 # This supports the ranging in the read.config files
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52 #If no range is given then the result is just one index of the given name
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53 def funcGetIndices(lsFeature, lsFunctionNames):
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54 if(len(lsFeature)) == 1:
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55 if(funcIsInt(lsFeature[0])):
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56 return int(lsFeature[0])-1
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57 return [lsFeatureNames.index(lsFeature[0])]
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58 if(len(lsFeature)) == 2:
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59 iIndices = []
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60 iPosition = 1
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61 for sFeature in lsFeature:
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62 if(sFeature==""):
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63 if(iPosition==1):
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64 iIndices.append(2)
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65 elif(iPosition==2):
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66 iIndices.append(len(lsFunctionNames)-1)
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67 elif(funcIsInt(sFeature)):
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68 iIndices.append(int(sFeature)-1)
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69 else:
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70 iIndices.append(lsFeatureNames.index(sFeature))
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71 iPosition = iPosition + 1
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72 return iIndices
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73
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74 #Constants
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75 #The line indicating the rows to read
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76 c_MatrixName = "Matrix:"
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77 c_DataMatrix = "Abundance"
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78 c_strRows = "Read_PCL_Rows:"
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79
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80 #Set up arguments reader
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81 argp = argparse.ArgumentParser( prog = "PCLToGraphlanCoreGene.py",
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82 description = """Converts PCL files to Graphlan core gene files.""" )
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83
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84 #Arguments
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85 argp.add_argument("strInputPCL", metavar = "PCLFile", type = argparse.FileType("r"), help ="Input PCl file used in maaslin")
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86 argp.add_argument("strInputRC", metavar = "RCFile", type = argparse.FileType("r"), help ="Input read config file used in maaslin")
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87 argp.add_argument("strOutputCoreGene", metavar = "CoreGeneFile", type = argparse.FileType("w"), help ="Output core gene file for graphlan")
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88
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89 args = argp.parse_args( )
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90
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91 #Read in read config table and get the rows/columns to use
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92 #Indicates if we are reading a data matrix
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93 fIsData = False
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94 #Holds the indices ranges
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95 #List of lists,each internal list hold 1 or 2 indices, if two it indicates a range from the first to the second
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96 llsIndices = []
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97 csvRC = open(args.strInputRC,'r') if isinstance(args.strInputRC, str) else args.strInputRC
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98 fRC = csv.reader(csvRC, delimiter=" ")
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99 for sLine in fRC:
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100 #Get the row indices or names
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101 if len(sLine):
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102 if sLine[0] == c_MatrixName:
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103 fIsData = sLine[1] == c_DataMatrix
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104 if sLine[0] == c_strRows:
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105 if fIsData:
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106 llsIndices = [sIndexRange.split("-") for sIndexRange in sLine[1].split(",")]
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107 break
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108 csvRC.close()
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109
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110 # Check to make sure RC file is read
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111 if len(llsIndices)==0:
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112 print("PCLToGraphlanCoreGene:: Could Not find indices in RC file "+args.strInputRC+".")
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113
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114 #Read in the PCL file and parse the file names to core genes format
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115 csvPCL = open(args.strInputPCL,'r') if isinstance(args.strInputPCL, str) else args.strInputPCL
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116 fPCL = csv.reader(csvPCL,delimiter="\t")
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117 #The first column of the csv file
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118 lsFeatureNames = [sLine[0] for sLine in fPCL]
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119 csvPCL.close()
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120
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121 # Check to make sure PCL file is read
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122 if len(lsFeatureNames)==0:
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123 print("PCLToGraphlanCoreGene:: Could Not find features in PCL file "+args.strInputPCL+".")
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124
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125 #If the indices are names switch with numbers otherwise subtract 1 because they are ment for R
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126 liConvertedRangedIndices = [funcGetIndices(sIndex,lsFeatureNames) for sIndex in llsIndices] if len(llsIndices)>0 else []
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127 llsIndices = None
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128
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129 #If there are any ranges, reduce to lists of indices
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130 liConvertedIndices = []
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131 for lsIndices in liConvertedRangedIndices:
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132 lsIndices.sort()
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133 iLenIndices = len(lsIndices)
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134 if iLenIndices > 2:
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135 print "Error, received more than 2 indices in a range. Stopped."
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136 exit()
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137 liConvertedIndices.extend(lsIndices if iLenIndices == 1 else range(lsIndices[0],lsIndices[1]+1))
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138 liConvertedRangedIndices = None
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139
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140 #Collapse all indices to a set which is then sorted
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141 liConvertedIndices = sorted(list(set(liConvertedIndices)))
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142
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143 #Reduce name of features to just bugs indicated by indices
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144 lsFeatureNames = itemgetter(*liConvertedIndices)(lsFeatureNames)
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145 liConvertedIndices = None
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146
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147 #Change the bug names to the correct formatting (clades seperated by .)
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148 lsFeatureNames = sorted(lsFeatureNames)
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149 lsFeatureNames = [re.sub("^[A-Za-z]__","",sBug) for sBug in lsFeatureNames]
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150 lsFeatureNames = [[re.sub("\|*[A-Za-z]__|\|",".",sBug)] for sBug in lsFeatureNames]
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151
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152 #If this is an OTU, append the number and the genus level together for a more descriptive termal name
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153 lsFeatureNamesModForOTU = []
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154 for sBug in lsFeatureNames:
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155 lsBug = sBug[0].split(".")
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156 if(len(lsBug))> 1:
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157 if(lsBug[-1].isdigit()):
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158 lsBug[-2]=lsBug[-2]+"_"+lsBug[-1]
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159 lsBug = lsBug[0:-1]
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160 lsFeatureNamesModForOTU.append([".".join(lsBug)])
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161 else:
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162 lsFeatureNamesModForOTU.append([lsBug[0]])
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163
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164 #Output core gene file
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165 csvCG = open(args.strOutputCoreGene,'w') if isinstance(args.strOutputCoreGene, str) else args.strOutputCoreGene
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166 fCG = csv.writer(csvCG)
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167 fCG.writerows(lsFeatureNamesModForOTU)
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168 csvCG.close()
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