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comparison maaslin-4450aa4ecc84/maaslin-4450aa4ecc84/src/PCLToGraphlanCoreGene.py @ 6:ca61989bc3b4

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author george-weingart
date Sun, 08 Feb 2015 23:39:43 -0500
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1 #!/usr/bin/env python
2 #####################################################################################
3 #Copyright (C) <2012>
4 #
5 #Permission is hereby granted, free of charge, to any person obtaining a copy of
6 #this software and associated documentation files (the "Software"), to deal in the
7 #Software without restriction, including without limitation the rights to use, copy,
8 #modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
9 #and to permit persons to whom the Software is furnished to do so, subject to
10 #the following conditions:
11 #
12 #The above copyright notice and this permission notice shall be included in all copies
13 #or substantial portions of the Software.
14 #
15 #THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
16 #INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
17 #PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
18 #HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
19 #OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
20 #SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
21 #
22 # This file is a component of the MaAsLin (Multivariate Associations Using Linear Models),
23 # authored by the Huttenhower lab at the Harvard School of Public Health
24 # (contact Timothy Tickle, ttickle@hsph.harvard.edu).
25 #####################################################################################
26
27 __author__ = "Timothy Tickle"
28 __copyright__ = "Copyright 2012"
29 __credits__ = ["Timothy Tickle"]
30 __license__ = ""
31 __version__ = ""
32 __maintainer__ = "Timothy Tickle"
33 __email__ = "ttickle@sph.harvard.edu"
34 __status__ = "Development"
35
36 import argparse
37 import csv
38 from operator import itemgetter
39 import re
40 import sys
41
42 #Helper function which returns a boolean indicator of an input string being parsable as an int
43 def funcIsInt(strInt):
44 try:
45 int(strInt)
46 return True
47 except:
48 return False
49
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
51 # This supports the ranging in the read.config files
52 #If no range is given then the result is just one index of the given name
53 def funcGetIndices(lsFeature, lsFunctionNames):
54 if(len(lsFeature)) == 1:
55 if(funcIsInt(lsFeature[0])):
56 return int(lsFeature[0])-1
57 return [lsFeatureNames.index(lsFeature[0])]
58 if(len(lsFeature)) == 2:
59 iIndices = []
60 iPosition = 1
61 for sFeature in lsFeature:
62 if(sFeature==""):
63 if(iPosition==1):
64 iIndices.append(2)
65 elif(iPosition==2):
66 iIndices.append(len(lsFunctionNames)-1)
67 elif(funcIsInt(sFeature)):
68 iIndices.append(int(sFeature)-1)
69 else:
70 iIndices.append(lsFeatureNames.index(sFeature))
71 iPosition = iPosition + 1
72 return iIndices
73
74 #Constants
75 #The line indicating the rows to read
76 c_MatrixName = "Matrix:"
77 c_DataMatrix = "Abundance"
78 c_strRows = "Read_PCL_Rows:"
79
80 #Set up arguments reader
81 argp = argparse.ArgumentParser( prog = "PCLToGraphlanCoreGene.py",
82 description = """Converts PCL files to Graphlan core gene files.""" )
83
84 #Arguments
85 argp.add_argument("strInputPCL", metavar = "PCLFile", type = argparse.FileType("r"), help ="Input PCl file used in maaslin")
86 argp.add_argument("strInputRC", metavar = "RCFile", type = argparse.FileType("r"), help ="Input read config file used in maaslin")
87 argp.add_argument("strOutputCoreGene", metavar = "CoreGeneFile", type = argparse.FileType("w"), help ="Output core gene file for graphlan")
88
89 args = argp.parse_args( )
90
91 #Read in read config table and get the rows/columns to use
92 #Indicates if we are reading a data matrix
93 fIsData = False
94 #Holds the indices ranges
95 #List of lists,each internal list hold 1 or 2 indices, if two it indicates a range from the first to the second
96 llsIndices = []
97 csvRC = open(args.strInputRC,'r') if isinstance(args.strInputRC, str) else args.strInputRC
98 fRC = csv.reader(csvRC, delimiter=" ")
99 for sLine in fRC:
100 #Get the row indices or names
101 if len(sLine):
102 if sLine[0] == c_MatrixName:
103 fIsData = sLine[1] == c_DataMatrix
104 if sLine[0] == c_strRows:
105 if fIsData:
106 llsIndices = [sIndexRange.split("-") for sIndexRange in sLine[1].split(",")]
107 break
108 csvRC.close()
109
110 # Check to make sure RC file is read
111 if len(llsIndices)==0:
112 print("PCLToGraphlanCoreGene:: Could Not find indices in RC file "+args.strInputRC+".")
113
114 #Read in the PCL file and parse the file names to core genes format
115 csvPCL = open(args.strInputPCL,'r') if isinstance(args.strInputPCL, str) else args.strInputPCL
116 fPCL = csv.reader(csvPCL,delimiter="\t")
117 #The first column of the csv file
118 lsFeatureNames = [sLine[0] for sLine in fPCL]
119 csvPCL.close()
120
121 # Check to make sure PCL file is read
122 if len(lsFeatureNames)==0:
123 print("PCLToGraphlanCoreGene:: Could Not find features in PCL file "+args.strInputPCL+".")
124
125 #If the indices are names switch with numbers otherwise subtract 1 because they are ment for R
126 liConvertedRangedIndices = [funcGetIndices(sIndex,lsFeatureNames) for sIndex in llsIndices] if len(llsIndices)>0 else []
127 llsIndices = None
128
129 #If there are any ranges, reduce to lists of indices
130 liConvertedIndices = []
131 for lsIndices in liConvertedRangedIndices:
132 lsIndices.sort()
133 iLenIndices = len(lsIndices)
134 if iLenIndices > 2:
135 print "Error, received more than 2 indices in a range. Stopped."
136 exit()
137 liConvertedIndices.extend(lsIndices if iLenIndices == 1 else range(lsIndices[0],lsIndices[1]+1))
138 liConvertedRangedIndices = None
139
140 #Collapse all indices to a set which is then sorted
141 liConvertedIndices = sorted(list(set(liConvertedIndices)))
142
143 #Reduce name of features to just bugs indicated by indices
144 lsFeatureNames = itemgetter(*liConvertedIndices)(lsFeatureNames)
145 liConvertedIndices = None
146
147 #Change the bug names to the correct formatting (clades seperated by .)
148 lsFeatureNames = sorted(lsFeatureNames)
149 lsFeatureNames = [re.sub("^[A-Za-z]__","",sBug) for sBug in lsFeatureNames]
150 lsFeatureNames = [[re.sub("\|*[A-Za-z]__|\|",".",sBug)] for sBug in lsFeatureNames]
151
152 #If this is an OTU, append the number and the genus level together for a more descriptive termal name
153 lsFeatureNamesModForOTU = []
154 for sBug in lsFeatureNames:
155 lsBug = sBug[0].split(".")
156 if(len(lsBug))> 1:
157 if(lsBug[-1].isdigit()):
158 lsBug[-2]=lsBug[-2]+"_"+lsBug[-1]
159 lsBug = lsBug[0:-1]
160 lsFeatureNamesModForOTU.append([".".join(lsBug)])
161 else:
162 lsFeatureNamesModForOTU.append([lsBug[0]])
163
164 #Output core gene file
165 csvCG = open(args.strOutputCoreGene,'w') if isinstance(args.strOutputCoreGene, str) else args.strOutputCoreGene
166 fCG = csv.writer(csvCG)
167 fCG.writerows(lsFeatureNamesModForOTU)
168 csvCG.close()