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1 #!/usr/bin/env python
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2 """
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3 Authors: Timothy Tickle and Curtis Huttenhower
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4 Description: Find associations in two matrices of data.
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5 """
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6
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7 __author__ = "Timothy Tickle and Curtis Huttenhower"
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8 __copyright__ = "Copyright 2012"
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9 __credits__ = ["Timothy Tickle","Curtis Huttenhower"]
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10 __maintainer__ = "Timothy Tickle"
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11 __email__ = "ttickle@hsph.harvard.edu"
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12
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13 import argparse
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14 import os
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15 import sfle
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16 import sys
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17
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18 c_strSufRC = ".read.config"
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19
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20 c_fileDirSrc = Dir( sfle.d( os.path.dirname( sfle.current_file( ) ), sfle.c_strDirSrc ) )
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21 c_fileProgMaaslin = File( sfle.d( c_fileDirSrc, "Maaslin.R" ) )
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22 sArgsExt = ".args"
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23 #Commandline to ignore
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24 lsIgnore = ["-i","-I","--input_config","--input_process"]
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25
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26 def MaAsLin( filePCL ):
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27 #Build input file name if they exist or give ""
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28 strBase = filePCL.get_abspath().replace( sfle.c_strSufPCL, "" )
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29 strR, strRC, strArgs = (( strBase + s ) for s in (sfle.c_strSufR, c_strSufRC, sArgsExt))
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30 fileR, fileRC, fileArgs = (( File( s ) if os.path.exists( s ) else "" ) for s in (strR, strRC, strArgs))
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31
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32 ## Read in an args file if it exists
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33 lsArgs = []
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34 if fileArgs:
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35 fReader = csv.reader(open(fileArgs.get_abspath(),'r'), delimiter = " ")
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36 lsArgsTmp = []
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37 [lsArgsTmp.extend(lsLine) for lsLine in fReader]
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38 fSkip = False
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39 for s in lsArgsTmp:
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40 if s in lsIgnore:
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41 fSkip=True
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42 continue
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43 if fSkip:
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44 fSkip = not fSkip
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45 continue
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46 lsArgs.append(s)
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47
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48 lsInputArgs = ["-I",[fileR]] if fileR else []
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49 lsInputArgs.extend(["-i",[fileRC]] if fileRC else [])
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50 lsArgs.extend(lsInputArgs)
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51
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52 strBase = os.path.basename( strBase )
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53 fileTSVFile = File(sfle.d(fileDirTmp,sfle.rebase(filePCL,sfle.c_strSufPCL,sfle.c_strSufTSV)))
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54 strT = File( sfle.d( os.path.join(fileDirOutput.get_abspath(), strBase, strBase + sfle.c_strSufTXT) ) )
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55
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56 #Transpose PCL
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57 sfle.spipe(pE, filePCL, c_fileProgTranspose, fileTSVFile)
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58 #Run MaAsLin
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59 sfle.op(pE, c_fileProgMaaslin, lsArgs+[[True,strT],[False, fileTSVFile]])
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60 if fileArgs: Depends(c_fileProgMaaslin, fileArgs)
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61 Default(strT) |
