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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 import math
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39 from operator import itemgetter
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40 import re
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41 import string
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42 import sys
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43
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44 #def funcGetColor(fNumeric,fMax):
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45 # if fNumeric>0:
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46 # return("#"+str(int(99*fNumeric/fMax)).zfill(2)+"0000")
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47 # if fNumeric<0:
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48 # return("#00"+str(int(99*abs(fNumeric/fMax))).zfill(2)+"00")
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49 # return("#000000")
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50
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51 def funcGetColor(fNumeric):
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52 if fNumeric>0:
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53 return sRingPositiveColor
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54 else:
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55 return sRingNegativeColor
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56
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57 def funcGetAlpha(fNumeric,fMax):
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58 return max(abs(fNumeric/fMax),dMinAlpha)
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59
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60 #Constants
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61 sAnnotation = "annotation"
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62 sAnnotationColor = "annotation_background_color"
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63 sClass = "class"
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64 sRingAlpha = "ring_alpha"
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65 dMinAlpha = .075
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66 sRingColor = "ring_color"
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67 sRingHeight = "ring_height"
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68 #sRingHeightMin = 0.5
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69 sStandardizedRingHeight = "1.01"
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70 sRingLabel = "ring_label"
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71 sRingLabelSizeWord = "ring_label_font_size"
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72 sRingLabelSize = 10
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73 sRingLineColor = "#999999"
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74 sRingPositiveWord = "Positive"
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75 sRingPositiveColor = "#990000"
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76 sRingNegativeWord = "Negative"
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77 sRingNegativeColor = "#009900"
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78 sRingLineColorWord = "ring_separator_color"
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79 sRingLineThickness = "0.5"
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80 sRingLineThicknessWord = "ring_internal_separator_thickness"
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81 sCladeMarkerColor = "clade_marker_color"
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82 sCladeMarkerSize = "clade_marker_size"
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83 sHighlightedMarkerSize = "10"
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84 c_dMinDoubleValue = 0.00000000001
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85
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86 #Set up arguments reader
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87 argp = argparse.ArgumentParser( prog = "MaaslinToGraphlanAnnotation.py",
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88 description = """Converts summary files to graphlan annotation files.""" )
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89
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90 #### Read in information
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91 #Arguments
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92 argp.add_argument("strInputSummary", metavar = "SummaryFile", type = argparse.FileType("r"), help ="Input summary file produced by maaslin")
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93 argp.add_argument("strInputCore", metavar = "CoreFile", type = argparse.FileType("r"), help ="Core file produced by Graphlan from the maaslin pcl")
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94 argp.add_argument("strInputHeader", metavar = "HeaderFile", type = argparse.FileType("r"), help ="Input header file to append to the generated annotation file.")
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95 argp.add_argument("strOutputAnnotation", metavar = "AnnotationFile", type = argparse.FileType("w"), help ="Output annotation file for graphlan")
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96
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97 args = argp.parse_args( )
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98
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99 #Read in the summary file and transform to class based descriptions
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100 csvSum = open(args.strInputSummary,'r') if isinstance(args.strInputSummary, str) else args.strInputSummary
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101 fSum = csv.reader(csvSum, delimiter="\t")
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102 #Skip header (until i do this a better way)
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103 fSum.next()
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104
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105 #Extract associations (Metadata,taxon,coef,qvalue)
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106 lsAssociations = [[sLine[1],sLine[2],sLine[4],sLine[7]] for sLine in fSum]
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107 csvSum.close()
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108
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109 #### Read in default graphlan settings provided by maaslin
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110 #Read in the annotation header file
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111 csvHdr = open(args.strInputHeader,'r') if isinstance(args.strInputHeader, str) else args.strInputHeader
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112 fHdr = csv.reader(csvHdr, delimiter="\t")
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113
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114 #Begin writting the output
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115 #Output annotation file
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116 csvAnn = open(args.strOutputAnnotation,'w') if isinstance(args.strOutputAnnotation, str) else args.strOutputAnnotation
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117 fAnn = csv.writer(csvAnn, delimiter="\t")
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118 fAnn.writerows(fHdr)
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119 csvHdr.close()
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120
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121 #If no associatiosn were found
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122 if(len(lsAssociations)==0):
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123 csvAnn.close()
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124
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125 else:
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126 #### Fix name formats
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127 #Manipulate names to graphlan complient names (clades seperated by .)
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128 lsAssociations = sorted(lsAssociations, key=itemgetter(1))
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129 lsAssociations = [[sBug[0]]+[re.sub("^[A-Za-z]__","",sBug[1])]+sBug[2:] for sBug in lsAssociations]
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130 lsAssociations = [[sBug[0]]+[re.sub("\|*[A-Za-z]__|\|",".",sBug[1])]+sBug[2:] for sBug in lsAssociations]
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131
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132 #If this is an OTU, append the number and the genus level together for a more descriptive termal name
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133 lsAssociationsModForOTU = []
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134 for sBug in lsAssociations:
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135 lsBug = sBug[1].split(".")
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136 if(len(lsBug))> 1:
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137 if(lsBug[-1].isdigit()):
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138 lsBug[-2]=lsBug[-2]+"_"+lsBug[-1]
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139 lsBug = lsBug[0:-1]
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140 lsAssociationsModForOTU.append([sBug[0]]+[".".join(lsBug)]+sBug[2:])
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141 else:
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142 lsAssociationsModForOTU.append([sBug[0]]+[lsBug[0]]+sBug[2:])
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143
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144 #Extract just class info
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145 #lsClassData = [[sLine[2],sClass,sLine[1]] for sLine in fSum]
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146
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147 ### Make rings
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148 #Setup rings
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149 dictRings = dict([[enumData[1],enumData[0]] for enumData in enumerate(set([lsData[0] for lsData in lsAssociationsModForOTU]))])
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150
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151 #Ring graphlan setting: rings represent a metadata that associates with a feature
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152 #Rings have a line to help differetiate them
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153 lsRingSettings = [[sRingLabel,lsPair[1],lsPair[0]] for lsPair in dictRings.items()]
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154 lsRingLineColors = [[sRingLineColorWord,lsPair[1],sRingLineColor] for lsPair in dictRings.items()]
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155 lsRingLineThick = [[sRingLineThicknessWord,lsPair[1],sRingLineThickness] for lsPair in dictRings.items()]
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156 lsRingLineLabelSize = [[sRingLabelSizeWord,lsPair[1], sRingLabelSize] for lsPair in dictRings.items()]
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157
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158 #Create coloring for rings color represents the directionality of the relationship
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159 dMaxCoef = max([abs(float(sAssociation[2])) for sAssociation in lsAssociationsModForOTU])
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160 lsRingColors = [[lsAssociation[1], sRingColor, dictRings[lsAssociation[0]], funcGetColor(float(lsAssociation[2]))] for lsAssociation in lsAssociationsModForOTU]
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161 lsRingAlpha = [[lsAssociation[1], sRingAlpha, dictRings[lsAssociation[0]], funcGetAlpha(float(lsAssociation[2]), dMaxCoef)] for lsAssociation in lsAssociationsModForOTU]
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162
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163 #Create height for rings representing the log tranformed q-value?
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164 dMaxQValue = max([-1*math.log(max(float(sAssociation[3]), c_dMinDoubleValue)) for sAssociation in lsAssociationsModForOTU])
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165 #lsRingHeights = [[lsAssociation[1], sRingHeight, dictRings[lsAssociation[0]], ((-1*math.log(max(float(lsAssociation[3]), c_dMinDoubleValue)))/dMaxQValue)+sRingHeightMin] for lsAssociation in lsAssociationsModForOTU]
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166 lsRingHeights = [[lsAssociation[1], sRingHeight, dictRings[lsAssociation[0]], sStandardizedRingHeight] for lsAssociation in lsAssociationsModForOTU]
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167
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168 #### Marker
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169 # Marker colors (mainly to make legend
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170 lsMarkerColors = [[lsAssociation[1], sCladeMarkerColor, funcGetColor(float(lsAssociation[2]))] for lsAssociation in lsAssociationsModForOTU]
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171 lsMarkerSizes = [[lsAssociation[1], sCladeMarkerSize, sHighlightedMarkerSize] for lsAssociation in lsAssociationsModForOTU]
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172
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173 #### Make internal highlights
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174 #Highlight the associated clades
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175 lsUniqueAssociatedTaxa = sorted(list(set([lsAssociation[1] for lsAssociation in lsAssociationsModForOTU])))
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176
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177 lsHighlights = []
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178 sABCPrefix = ""
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179 sListABC = string.ascii_lowercase
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180 iListABCIndex = 0
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181 for lsHighlight in lsUniqueAssociatedTaxa:
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182 lsTaxa = lsHighlight.split(".")
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183 sLabel = sABCPrefix+sListABC[iListABCIndex]+":"+lsTaxa[-1] if len(lsTaxa) > 2 else lsTaxa[-1]
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184 lsHighlights.append([lsHighlight, sAnnotation, sLabel])
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185 iListABCIndex = iListABCIndex + 1
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186 if iListABCIndex > 25:
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187 iListABCIndex = 0
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188 sABCPrefix = sABCPrefix + sListABC[len(sABCPrefix)]
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189
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190 #Read in the core file
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191 csvCore = open(args.strInputCore,'r') if isinstance(args.strInputCore, str) else args.strInputCore
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192 fSum = csv.reader(csvCore, delimiter="\t")
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193
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194 #Add in all phylum just incase they were not already included here
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195 lsAddSecondLevel = list(set([sUnique[0].split(".")[1] for sUnique in fSum if len(sUnique[0].split(".")) > 1]))
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196 lsHighlights.extend([[sSecondLevel, sAnnotation, sSecondLevel] for sSecondLevel in lsAddSecondLevel])
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197 lsHighlightColor = [[lsHighlight[0], sAnnotationColor,"b"] for lsHighlight in lsHighlights]
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198
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199 #### Write the remaining output annotation file
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200 fAnn.writerows(lsRingSettings)
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201 fAnn.writerows(lsRingLineColors)
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202 fAnn.writerows(lsRingColors)
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203 fAnn.writerows(lsRingAlpha)
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204 fAnn.writerows(lsRingLineThick)
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205 fAnn.writerows(lsRingLineLabelSize)
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206 fAnn.writerows(lsRingHeights)
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207 fAnn.writerows(lsMarkerColors)
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208 fAnn.writerows(lsMarkerSizes)
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209 fAnn.writerows([[sRingPositiveWord, sCladeMarkerColor, sRingPositiveColor]])
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210 fAnn.writerows([[sRingNegativeWord, sCladeMarkerColor, sRingNegativeColor]])
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211 fAnn.writerows(lsHighlights)
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212 fAnn.writerows(lsHighlightColor)
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213 csvAnn.close()
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