Mercurial > repos > sagun98 > micropita
comparison galaxy_micropita/src/breadcrumbs/scripts/scriptConvertBetweenBIOMAndPCL.py @ 3:8fb4630ab314 draft default tip
Uploaded
| author | sagun98 |
|---|---|
| date | Thu, 03 Jun 2021 17:07:36 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 2:1c5736dc85ab | 3:8fb4630ab314 |
|---|---|
| 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) |