maaslin: maaslin-4450aa4ecc84/src/MaaslinToGraphlanAnnotation.py annotate

annotate maaslin-4450aa4ecc84/src/MaaslinToGraphlanAnnotation.py @ 1:a87d5a5f2776

Uploaded the version running on the prod server

author	george-weingart
date	Sun, 08 Feb 2015 23:08:38 -0500
parents
children

rev	line source
1 a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	1 #!/usr/bin/env python
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	2 #####################################################################################
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	3 #Copyright (C) <2012>
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	4 #
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	5 #Permission is hereby granted, free of charge, to any person obtaining a copy of
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	6 #this software and associated documentation files (the "Software"), to deal in the
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	7 #Software without restriction, including without limitation the rights to use, copy,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	8 #modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	9 #and to permit persons to whom the Software is furnished to do so, subject to
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	10 #the following conditions:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	11 #
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	12 #The above copyright notice and this permission notice shall be included in all copies
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	13 #or substantial portions of the Software.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	14 #
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	15 #THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	16 #INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	17 #PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	18 #HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	19 #OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	20 #SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	21 #
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	22 # This file is a component of the MaAsLin (Multivariate Associations Using Linear Models),
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	23 # authored by the Huttenhower lab at the Harvard School of Public Health
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	24 # (contact Timothy Tickle, ttickle@hsph.harvard.edu).
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	25 #####################################################################################
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	26
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	27 __author__ = "Timothy Tickle"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	28 __copyright__ = "Copyright 2012"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	29 __credits__ = ["Timothy Tickle"]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	30 __license__ = ""
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	31 __version__ = ""
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	32 __maintainer__ = "Timothy Tickle"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	33 __email__ = "ttickle@sph.harvard.edu"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	34 __status__ = "Development"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	35
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	36 import argparse
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	37 import csv
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	38 import math
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	39 from operator import itemgetter
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	40 import re
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	41 import string
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	42 import sys
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	43
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	44 #def funcGetColor(fNumeric,fMax):
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	45 # if fNumeric>0:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	46 # return("#"+str(int(99*fNumeric/fMax)).zfill(2)+"0000")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	47 # if fNumeric<0:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	48 # return("#00"+str(int(99*abs(fNumeric/fMax))).zfill(2)+"00")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	49 # return("#000000")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	50
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	51 def funcGetColor(fNumeric):
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	52 if fNumeric>0:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	53 return sRingPositiveColor
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	54 else:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	55 return sRingNegativeColor
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	56
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	57 def funcGetAlpha(fNumeric,fMax):
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	58 return max(abs(fNumeric/fMax),dMinAlpha)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	59
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	60 #Constants
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	61 sAnnotation = "annotation"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	62 sAnnotationColor = "annotation_background_color"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	63 sClass = "class"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	64 sRingAlpha = "ring_alpha"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	65 dMinAlpha = .075
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	66 sRingColor = "ring_color"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	67 sRingHeight = "ring_height"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	68 #sRingHeightMin = 0.5
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	69 sStandardizedRingHeight = "1.01"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	70 sRingLabel = "ring_label"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	71 sRingLabelSizeWord = "ring_label_font_size"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	72 sRingLabelSize = 10
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	73 sRingLineColor = "#999999"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	74 sRingPositiveWord = "Positive"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	75 sRingPositiveColor = "#990000"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	76 sRingNegativeWord = "Negative"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	77 sRingNegativeColor = "#009900"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	78 sRingLineColorWord = "ring_separator_color"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	79 sRingLineThickness = "0.5"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	80 sRingLineThicknessWord = "ring_internal_separator_thickness"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	81 sCladeMarkerColor = "clade_marker_color"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	82 sCladeMarkerSize = "clade_marker_size"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	83 sHighlightedMarkerSize = "10"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	84 c_dMinDoubleValue = 0.00000000001
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	85
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	86 #Set up arguments reader
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	87 argp = argparse.ArgumentParser( prog = "MaaslinToGraphlanAnnotation.py",
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	88 description = """Converts summary files to graphlan annotation files.""" )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	89
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	90 #### Read in information
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	91 #Arguments
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	92 argp.add_argument("strInputSummary", metavar = "SummaryFile", type = argparse.FileType("r"), help ="Input summary file produced by maaslin")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	93 argp.add_argument("strInputCore", metavar = "CoreFile", type = argparse.FileType("r"), help ="Core file produced by Graphlan from the maaslin pcl")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	94 argp.add_argument("strInputHeader", metavar = "HeaderFile", type = argparse.FileType("r"), help ="Input header file to append to the generated annotation file.")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	95 argp.add_argument("strOutputAnnotation", metavar = "AnnotationFile", type = argparse.FileType("w"), help ="Output annotation file for graphlan")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	96
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	97 args = argp.parse_args( )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	98
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	99 #Read in the summary file and transform to class based descriptions
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	100 csvSum = open(args.strInputSummary,'r') if isinstance(args.strInputSummary, str) else args.strInputSummary
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	101 fSum = csv.reader(csvSum, delimiter="\t")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	102 #Skip header (until i do this a better way)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	103 fSum.next()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	104
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	105 #Extract associations (Metadata,taxon,coef,qvalue)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	106 lsAssociations = [[sLine[1],sLine[2],sLine[4],sLine[7]] for sLine in fSum]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	107 csvSum.close()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	108
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	109 #### Read in default graphlan settings provided by maaslin
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	110 #Read in the annotation header file
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	111 csvHdr = open(args.strInputHeader,'r') if isinstance(args.strInputHeader, str) else args.strInputHeader
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	112 fHdr = csv.reader(csvHdr, delimiter="\t")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	113
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	114 #Begin writting the output
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	115 #Output annotation file
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	116 csvAnn = open(args.strOutputAnnotation,'w') if isinstance(args.strOutputAnnotation, str) else args.strOutputAnnotation
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	117 fAnn = csv.writer(csvAnn, delimiter="\t")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	118 fAnn.writerows(fHdr)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	119 csvHdr.close()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	120
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	121 #If no associatiosn were found
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	122 if(len(lsAssociations)==0):
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	123 csvAnn.close()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	124
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	125 else:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	126 #### Fix name formats
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	127 #Manipulate names to graphlan complient names (clades seperated by .)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	128 lsAssociations = sorted(lsAssociations, key=itemgetter(1))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	129 lsAssociations = [[sBug[0]]+[re.sub("^[A-Za-z]__","",sBug[1])]+sBug[2:] for sBug in lsAssociations]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	130 lsAssociations = [[sBug[0]]+[re.sub("\\|*[A-Za-z]__\|\\|",".",sBug[1])]+sBug[2:] for sBug in lsAssociations]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	131
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	132 #If this is an OTU, append the number and the genus level together for a more descriptive termal name
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	133 lsAssociationsModForOTU = []
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	134 for sBug in lsAssociations:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	135 lsBug = sBug[1].split(".")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	136 if(len(lsBug))> 1:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	137 if(lsBug[-1].isdigit()):
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	138 lsBug[-2]=lsBug[-2]+"_"+lsBug[-1]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	139 lsBug = lsBug[0:-1]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	140 lsAssociationsModForOTU.append([sBug[0]]+[".".join(lsBug)]+sBug[2:])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	141 else:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	142 lsAssociationsModForOTU.append([sBug[0]]+[lsBug[0]]+sBug[2:])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	143
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	144 #Extract just class info
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	145 #lsClassData = [[sLine[2],sClass,sLine[1]] for sLine in fSum]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	146
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	147 ### Make rings
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	148 #Setup rings
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	149 dictRings = dict([[enumData[1],enumData[0]] for enumData in enumerate(set([lsData[0] for lsData in lsAssociationsModForOTU]))])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	150
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	151 #Ring graphlan setting: rings represent a metadata that associates with a feature
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	152 #Rings have a line to help differetiate them
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	153 lsRingSettings = [[sRingLabel,lsPair[1],lsPair[0]] for lsPair in dictRings.items()]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	154 lsRingLineColors = [[sRingLineColorWord,lsPair[1],sRingLineColor] for lsPair in dictRings.items()]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	155 lsRingLineThick = [[sRingLineThicknessWord,lsPair[1],sRingLineThickness] for lsPair in dictRings.items()]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	156 lsRingLineLabelSize = [[sRingLabelSizeWord,lsPair[1], sRingLabelSize] for lsPair in dictRings.items()]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	157
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	158 #Create coloring for rings color represents the directionality of the relationship
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	159 dMaxCoef = max([abs(float(sAssociation[2])) for sAssociation in lsAssociationsModForOTU])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	160 lsRingColors = [[lsAssociation[1], sRingColor, dictRings[lsAssociation[0]], funcGetColor(float(lsAssociation[2]))] for lsAssociation in lsAssociationsModForOTU]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	161 lsRingAlpha = [[lsAssociation[1], sRingAlpha, dictRings[lsAssociation[0]], funcGetAlpha(float(lsAssociation[2]), dMaxCoef)] for lsAssociation in lsAssociationsModForOTU]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	162
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	163 #Create height for rings representing the log tranformed q-value?
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	164 dMaxQValue = max([-1*math.log(max(float(sAssociation[3]), c_dMinDoubleValue)) for sAssociation in lsAssociationsModForOTU])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	165 #lsRingHeights = [[lsAssociation[1], sRingHeight, dictRings[lsAssociation[0]], ((-1*math.log(max(float(lsAssociation[3]), c_dMinDoubleValue)))/dMaxQValue)+sRingHeightMin] for lsAssociation in lsAssociationsModForOTU]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	166 lsRingHeights = [[lsAssociation[1], sRingHeight, dictRings[lsAssociation[0]], sStandardizedRingHeight] for lsAssociation in lsAssociationsModForOTU]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	167
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	168 #### Marker
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	169 # Marker colors (mainly to make legend
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	170 lsMarkerColors = [[lsAssociation[1], sCladeMarkerColor, funcGetColor(float(lsAssociation[2]))] for lsAssociation in lsAssociationsModForOTU]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	171 lsMarkerSizes = [[lsAssociation[1], sCladeMarkerSize, sHighlightedMarkerSize] for lsAssociation in lsAssociationsModForOTU]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	172
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	173 #### Make internal highlights
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	174 #Highlight the associated clades
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	175 lsUniqueAssociatedTaxa = sorted(list(set([lsAssociation[1] for lsAssociation in lsAssociationsModForOTU])))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	176
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	177 lsHighlights = []
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	178 sABCPrefix = ""
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	179 sListABC = string.ascii_lowercase
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	180 iListABCIndex = 0
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	181 for lsHighlight in lsUniqueAssociatedTaxa:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	182 lsTaxa = lsHighlight.split(".")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	183 sLabel = sABCPrefix+sListABC[iListABCIndex]+":"+lsTaxa[-1] if len(lsTaxa) > 2 else lsTaxa[-1]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	184 lsHighlights.append([lsHighlight, sAnnotation, sLabel])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	185 iListABCIndex = iListABCIndex + 1
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	186 if iListABCIndex > 25:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	187 iListABCIndex = 0
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	188 sABCPrefix = sABCPrefix + sListABC[len(sABCPrefix)]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	189
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	190 #Read in the core file
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	191 csvCore = open(args.strInputCore,'r') if isinstance(args.strInputCore, str) else args.strInputCore
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	192 fSum = csv.reader(csvCore, delimiter="\t")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	193
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	194 #Add in all phylum just incase they were not already included here
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	195 lsAddSecondLevel = list(set([sUnique[0].split(".")[1] for sUnique in fSum if len(sUnique[0].split(".")) > 1]))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	196 lsHighlights.extend([[sSecondLevel, sAnnotation, sSecondLevel] for sSecondLevel in lsAddSecondLevel])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	197 lsHighlightColor = [[lsHighlight[0], sAnnotationColor,"b"] for lsHighlight in lsHighlights]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	198
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	199 #### Write the remaining output annotation file
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	200 fAnn.writerows(lsRingSettings)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	201 fAnn.writerows(lsRingLineColors)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	202 fAnn.writerows(lsRingColors)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	203 fAnn.writerows(lsRingAlpha)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	204 fAnn.writerows(lsRingLineThick)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	205 fAnn.writerows(lsRingLineLabelSize)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	206 fAnn.writerows(lsRingHeights)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	207 fAnn.writerows(lsMarkerColors)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	208 fAnn.writerows(lsMarkerSizes)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	209 fAnn.writerows([[sRingPositiveWord, sCladeMarkerColor, sRingPositiveColor]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	210 fAnn.writerows([[sRingNegativeWord, sCladeMarkerColor, sRingNegativeColor]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	211 fAnn.writerows(lsHighlights)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	212 fAnn.writerows(lsHighlightColor)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	213 csvAnn.close()

Mercurial > repos > george-weingart > maaslin

annotate maaslin-4450aa4ecc84/src/MaaslinToGraphlanAnnotation.py @ 1:a87d5a5f2776