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comparison src/breadcrumbs/scripts/scriptConvertBetweenBIOMAndPCL.py @ 0:2f4f6f08c8c4 draft

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author george-weingart
date Tue, 13 May 2014 21:58:57 -0400
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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)