diff galaxy_micropita/src/breadcrumbs/scripts/scriptConvertBetweenBIOMAndPCL.py @ 3:8fb4630ab314 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_micropita/src/breadcrumbs/scripts/scriptConvertBetweenBIOMAndPCL.py	Thu Jun 03 17:07:36 2021 +0000
@@ -0,0 +1,55 @@
+#!/usr/bin/env python
+"""
+Author: Timothy Tickle
+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.
+"""
+
+__author__ = "Timothy Tickle"
+__copyright__ = "Copyright 2013"
+__credits__ = ["Timothy Tickle","George Weingart"]
+__license__ = ""
+__version__ = ""
+__maintainer__ = "Timothy Tickle"
+__email__ = "[e-mail]"
+__status__ = "Development"
+
+from AbundanceTable import AbundanceTable
+import argparse
+from ConstantsBreadCrumbs import ConstantsBreadCrumbs
+import os
+import sys
+
+
+#Set up arguments reader
+argp = argparse.ArgumentParser( prog = "convertBetweenBIOMAndPCL.py",
+    description = """Converts a PCL file to a BIOM file and visa versa.""" )
+
+#Arguments
+#For table
+argp.add_argument("-i","--id", dest="sID", default = None, metavar= "Sample ID", help="The metadata indicating the sample ID.")
+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.")
+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.")
+argp.add_argument("-f","--delim", dest = "cFileDelimiter", action= "store", metavar="File Delimiter", default="\t", help="File delimiter, default tab") 
+argp.add_argument("strFileAbund", metavar = "Abundance file", help ="Input data file")
+argp.add_argument("strOutputFile", default = "", nargs="?", metavar = "Selection Output File", help ="Output file")
+
+args = argp.parse_args( )
+
+# Make the output file name (if not given) and get the type of output file name
+# Change the extension from BIOM to pcl
+lsFilePieces = os.path.splitext(args.strFileAbund)
+strOutputFileType = ConstantsBreadCrumbs.c_strPCLFile if lsFilePieces[-1]=="."+ConstantsBreadCrumbs.c_strBiomFile else ConstantsBreadCrumbs.c_strBiomFile
+
+if not args.strOutputFile:
+  args.strOutputFile = lsFilePieces[0] + "." + strOutputFileType
+
+# Set the last metadata to the id if not given.
+if not args.sLastMetadataName:
+  args.sLastMetadataName = args.sID
+
+# Read in abundance table
+abndTable = AbundanceTable.funcMakeFromFile(args.strFileAbund, cDelimiter=args.cFileDelimiter, sMetadataID=args.sID, sLastMetadataRow = args.sLastMetadataRow, sLastMetadata=args.sLastMetadataName, xOutputFile=args.strOutputFile)
+if not abndTable:
+  print("Could not create an abundance table from the given file and settings.")
+else:
+  abndTable.funcWriteToFile(args.strOutputFile, cDelimiter=args.cFileDelimiter, cFileType=strOutputFileType)