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1 #!/usr/bin/env python
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2 """
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3 Author: Timothy Tickle
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4 Description: Converts between BIOM and PCL files. If a PCL file is read, an equivalent BIOM file will be written; if a BIOM file is read, an equivalent pcl file will be written.
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5 """
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6
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7 __author__ = "Timothy Tickle"
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8 __copyright__ = "Copyright 2013"
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9 __credits__ = ["Timothy Tickle","George Weingart"]
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10 __license__ = ""
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11 __version__ = ""
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12 __maintainer__ = "Timothy Tickle"
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13 __email__ = "ttickle@hsph.harvard.edu"
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14 __status__ = "Development"
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15
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16 from AbundanceTable import AbundanceTable
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17 import argparse
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18 from ConstantsBreadCrumbs import ConstantsBreadCrumbs
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19 import os
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20 import sys
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21
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22
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23 #Set up arguments reader
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24 argp = argparse.ArgumentParser( prog = "convertBetweenBIOMAndPCL.py",
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25 description = """Converts a PCL file to a BIOM file and visa versa.""" )
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26
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27 #Arguments
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28 #For table
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29 argp.add_argument("-i","--id", dest="sID", default = None, metavar= "Sample ID", help="The metadata indicating the sample ID.")
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30 argp.add_argument("-l","--meta", dest = "sLastMetadataName", default = None, metavar= "Last Metadata Name", help="The last listed metadata before the first data measurement in the pcl file or to be in the pcl file.")
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31 argp.add_argument("-r","--rowMetadataID", dest = "sLastMetadataRow", default = None, metavar = "Last Row Metadata Column", help = "If row metadata is present in a PCL file, what is the id of the last row metadata column (most right column that contains row metadata). PCL file only.")
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32 argp.add_argument("-f","--delim", dest = "cFileDelimiter", action= "store", metavar="File Delimiter", default="\t", help="File delimiter, default tab")
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33 argp.add_argument("strFileAbund", metavar = "Abundance file", help ="Input data file")
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34 argp.add_argument("strOutputFile", default = "", nargs="?", metavar = "Selection Output File", help ="Output file")
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35
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36 args = argp.parse_args( )
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37
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38 # Make the output file name (if not given) and get the type of output file name
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39 # Change the extension from BIOM to pcl
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40 lsFilePieces = os.path.splitext(args.strFileAbund)
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41 strOutputFileType = ConstantsBreadCrumbs.c_strPCLFile if lsFilePieces[-1]=="."+ConstantsBreadCrumbs.c_strBiomFile else ConstantsBreadCrumbs.c_strBiomFile
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42
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43 if not args.strOutputFile:
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44 args.strOutputFile = lsFilePieces[0] + "." + strOutputFileType
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45
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46 # Set the last metadata to the id if not given.
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47 if not args.sLastMetadataName:
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48 args.sLastMetadataName = args.sID
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49
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50 # Read in abundance table
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51 abndTable = AbundanceTable.funcMakeFromFile(args.strFileAbund, cDelimiter=args.cFileDelimiter, sMetadataID=args.sID, sLastMetadataRow = args.sLastMetadataRow, sLastMetadata=args.sLastMetadataName, xOutputFile=args.strOutputFile)
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52 if not abndTable:
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53 print("Could not create an abundance table from the given file and settings.")
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54 else:
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55 abndTable.funcWriteToFile(args.strOutputFile, cDelimiter=args.cFileDelimiter, cFileType=strOutputFileType)
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