--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_micropita/src/breadcrumbs/scripts/scriptPcoa.py	Thu Jun 03 17:07:36 2021 +0000
@@ -0,0 +1,143 @@
+#!/usr/bin/env python
+"""
+Author: Timothy Tickle
+Description: Make PCoA of an abundance file
+"""
+
+__author__ = "Timothy Tickle"
+__copyright__ = "Copyright 2012"
+__credits__ = ["Timothy Tickle"]
+__license__ = ""
+__version__ = ""
+__maintainer__ = "Timothy Tickle"
+__email__ = "ttickle@sph.harvard.edu"
+__status__ = "Development"
+
+import sys
+import argparse
+from src.AbundanceTable import AbundanceTable
+from src.Metric import Metric
+import csv
+import os
+from src.PCoA import PCoA
+
+#Set up arguments reader
+argp = argparse.ArgumentParser( prog = "scriptPcoa.py",
+    description = """PCoAs an abundance file given a metadata.\nExample:python scriptPcoa.py -i TID -l STSite""" )
+
+#Arguments
+#For table
+argp.add_argument("-i","--id", dest="sIDName", default="ID", help="Abundance Table ID")
+argp.add_argument("-l","--meta", dest="sLastMetadataName", help="Last metadata name")
+argp.add_argument("-d","--fDelim", dest= "cFileDelimiter", action= "store", default="\t", help="File delimiter, default tab")
+argp.add_argument("-f","--featureDelim", dest="cFeatureNameDelimiter", action= "store", metavar="Feature Name Delimiter", default="|", help="Feature delimiter") 
+
+argp.add_argument("-n","--doNorm", dest="fDoNormData", action="store_true", default=False, help="Flag to turn on normalization")
+argp.add_argument("-s","--doSum", dest="fDoSumData", action="store_true", default=False, help="Flag to turn on summation")
+
+argp.add_argument("-p","--paint", dest="sLabel", metavar= "Label", default=None, help="Label to paint in the PCoA")
+argp.add_argument("-m","--metric", dest="strMetric", metavar = "distance", default = PCoA.c_BRAY_CURTIS, help ="Distance metric to use. Pick from braycurtis, canberra, chebyshev, cityblock, correlation, cosine, euclidean, hamming, spearman, sqeuclidean, unifrac_unweighted, unifrac_weighted")
+argp.add_argument("-o","--outputFile", dest="strOutFile", metavar= "outputFile", default=None, help="Specify the path for the output figure.")
+argp.add_argument("-D","--DistanceMatrix", dest="strFileDistanceMatrix", metavar= "strFileDistanceMatrix", default=None, help="Specify the path for outputing the distance matrix (if interested). Default this will not output.")
+argp.add_argument("-C","--CoordinatesMatrix", dest="strFileCoordinatesMatrix", metavar= "strFileCoordinatesMatrix", default=None, help="Specify the path for outputing the x,y coordinates matrix (Dim 1 and 2). Default this will not output.")
+
+# Unifrac arguments
+argp.add_argument("-t","--unifracTree", dest="istrmTree", metavar="UnifracTreeFile", default=None, help="Optional file only needed for UniFrac calculations.")
+argp.add_argument("-e","--unifracEnv", dest="istrmEnvr", metavar="UnifracEnvFile", default=None, help="Optional file only needed for UniFrac calculations.")
+argp.add_argument("-c","--unifracColor", dest="fileUnifracColor", metavar="UnifracColorFile", default = None, help="A text file indicating the groupings of metadata to color. Each line in the file is a group to color. An example file line would be  'GroupName:ID,ID,ID,ID'")
+
+argp.add_argument("strFileAbund", metavar = "Abundance file", nargs="?", help ="Input data file")
+
+args = argp.parse_args( )
+
+#Read in abundance table
+abndTable = None
+if args.strFileAbund:
+  abndTable = AbundanceTable.funcMakeFromFile(args.strFileAbund,
+                             cDelimiter = args.cFileDelimiter,
+                             sMetadataID = args.sIDName,
+                             sLastMetadata = args.sLastMetadataName,
+                             cFeatureNameDelimiter= args.cFeatureNameDelimiter)
+
+  #Normalize if need
+  if args.fDoSumData:
+    abndTable.funcSumClades()
+
+  #Sum if needed
+  if args.fDoNormData:
+    abndTable.funcNormalize()
+
+#Get the metadata to paint
+lsKeys = None
+if abndTable:
+  lsKeys = abndTable.funcGetMetadataCopy().keys() if not args.sLabel else [args.sLabel]
+
+#Get pieces of output file
+if not args.strOutFile:
+  if not args.strFileAbund:
+    args.strOutFile = os.path.splitext(os.path.basename(args.istrmEnvr))[0]+"-pcoa.pdf"
+  else:
+    args.strOutFile = os.path.splitext(os.path.basename(args.strFileAbund))[0]+"-pcoa.pdf"
+lsFilePieces = os.path.splitext(args.strOutFile)
+
+# Make PCoA object
+# Get PCoA object and plot
+pcoa = PCoA()
+if(not args.strMetric in [Metric.c_strUnifracUnweighted,Metric.c_strUnifracWeighted]) and abndTable:
+  pcoa.loadData(abndTable,True)
+# Optional args.strFileDistanceMatrix if not none will force a printing of the distance measures to the path in args.strFileDistanceMatrix
+pcoa.run(tempDistanceMetric=args.strMetric, iDims=2, strDistanceMatrixFile=args.strFileDistanceMatrix, istrmTree=args.istrmTree, istrmEnvr=args.istrmEnvr)
+
+# Write dim 1 and 2 coordinates to file
+if args.strFileCoordinatesMatrix:
+  lsIds = pcoa.funcGetIDs()
+  mtrxCoordinates = pcoa.funcGetCoordinates()
+  csvrCoordinates = csv.writer(open(args.strFileCoordinatesMatrix, 'w'))
+  csvrCoordinates.writerow(["ID","Dimension_1","Dimension_2"])
+  for x in xrange(mtrxCoordinates.shape[0]):
+    strId = lsIds[x] if lsIds else ""
+    csvrCoordinates.writerow([strId]+mtrxCoordinates[x].tolist())
+
+# Paint metadata
+if lsKeys:
+  for iIndex in xrange(len(lsKeys)):
+    lsMetadata = abndTable.funcGetMetadata(lsKeys[iIndex])
+
+    pcoa.plotList(lsLabelList = lsMetadata,
+      strOutputFileName = lsFilePieces[0]+"-"+lsKeys[iIndex]+lsFilePieces[1],
+      iSize=20,
+      dAlpha=1.0,
+      charForceColor=None,
+      charForceShape=None,
+      fInvert=False,
+      iDim1=1,
+      iDim2=2)
+
+if args.strMetric in [Metric.c_strUnifracUnweighted,Metric.c_strUnifracWeighted]:
+
+  c_sNotGiven = "Not_specified"
+
+  lsIds = pcoa.funcGetIDs()
+  lsGroupLabels = [c_sNotGiven for s in lsIds]
+
+  if args.fileUnifracColor:
+
+    # Read color file and make a dictionary to convert ids
+    lsColorLines = csv.reader(open(args.fileUnifracColor))
+    dictConvertIDToGroup = {}
+    for lsLine in lsColorLines:
+      if lsLine:
+        sGroupID, sFirstID = lsLine[0].split(":")
+        dictConvertIDToGroup.update(dict([(sID,sGroupID) for sID in [sFirstID]+lsLine[1:]]))
+
+    lsGroupLabels = [dictConvertIDToGroup.get(sID,c_sNotGiven) for sID in lsIds]
+
+  pcoa.plotList(lsLabelList = lsGroupLabels,
+      strOutputFileName = lsFilePieces[0]+"-"+args.strMetric+lsFilePieces[1],
+      iSize=20,
+      dAlpha=1.0,
+      charForceColor=None,
+      charForceShape=None,
+      fInvert=False,
+      iDim1=1,
+      iDim2=2)