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