--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_micropita/src/breadcrumbs/scripts/scriptManipulateTable.py	Thu Jun 03 17:07:36 2021 +0000
@@ -0,0 +1,295 @@
+#!/usr/bin/env python
+"""
+Author: Timothy Tickle
+Description: Performs common manipulations on tables
+"""
+
+__author__ = "Timothy Tickle"
+__copyright__ = "Copyright 2012"
+__credits__ = ["Timothy Tickle"]
+__license__ = ""
+__version__ = ""
+__maintainer__ = "Timothy Tickle"
+__email__ = "ttickle@sph.harvard.edu"
+__status__ = "Development"
+
+import argparse
+import csv
+import sys
+import re
+import os
+import numpy as np
+from src.AbundanceTable import AbundanceTable
+#from src.PCA import PCA
+from src.ValidateData import ValidateData
+
+#Set up arguments reader
+argp = argparse.ArgumentParser( prog = "scriptManipulateTable.py",
+    description = """Performs common manipulations on tables.\nExample: python scriptManipulateTable.py -i TID -l STSite Test.pcl""" )
+
+#Arguments
+#Describe 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","--fileDelim", dest= "cFileDelimiter", action= "store", default="\t", help="File delimiter, default tab")
+argp.add_argument("-f","--featureDelim", dest= "cFeatureDelimiter", action= "store", default="|", help="Feature (eg. bug or function) delimiter, default '|'")
+
+#Checked x 2
+argp.add_argument("-n","--doNorm", dest="fNormalize", action="store_true", default=False, help="Flag to turn on normalization")
+argp.add_argument("-s","--doSum", dest="fSum", action="store_true", default=False, help="Flag to turn on summation")
+
+#Unsupervised filtering
+argp.add_argument("-A","--doFilterAbundance", dest="strFilterAbundance", action="store", default=None, help="Turns on filtering by abundance (remove features that do not have a minimum abundance in a minimum number of samples); Should be a real number and an integer in the form 'minAbundance,minSamples', (should be performed on a normalized file).")
+argp.add_argument("-P","--doFilterPercentile", dest="strFilterPercentile", action="store", default=None, help="Turns on filtering by percentile Should be two numbers between 0 and 1 in the form 'percentile,percentage'. (should be performed on a normalized file).")
+argp.add_argument("-O","--doFilterOccurrence", dest="strFilterOccurence", action="store", default=None, help="Turns on filtering by occurrence. Should be two integers in the form 'minSequence,minSample' (should NOT be performed on a normalized file).")
+#argp.add_argument("-D","--doFilterDeviation", dest="dCuttOff", action="store", type=float, default=None, help="Flag to turn on filtering by standard deviation (should NOT be performed on a normalized file).")
+
+#Change bug membership
+argp.add_argument("-t","--makeTerminal", dest="fMakeTerminal", action="store_true", default=False, help="Works reduces the file to teminal features in the original file.")
+argp.add_argument("-u","--reduceOTUs", dest="fRemoveOTUs", action="store_true", default=False, help="Remove otu entries from file.")
+argp.add_argument("-c","--reduceToClade", dest="iClade", action="store", type=int, default=None, help="Specify a level of clade to reduce to [].")
+argp.add_argument("-b","--reduceToFeatures", dest="strFeatures", action="store", default=None, help="Reduce measurements to certain features (bugs or functions). This can be a comma delimited string (of atleast 2 bugs) or a file.")
+
+#Manipulate based on metadata
+#Checked
+argp.add_argument("-y","--stratifyBy", dest="strStratifyBy", action="store", default=None, help="Metadata to stratify tables by.")
+argp.add_argument("-r","--removeMetadata", dest="strRemoveMetadata", action="store", default=None, help="Remove samples of this metadata and value (format comma delimited string with metadata id first and the values to remove after 'id,lvalue1,value2').")
+
+#Manipulate lineage
+#Checked
+argp.add_argument("-x","--doPrefixClades", dest="fPrefixClades", action="store_true", default=False, help="Flag to turn on adding prefixes to clades to better identify them, for example s__ will be placed infront of each species.")
+
+#Combine tables
+#argp.add_argument("-m","--combineIntersect", dest="fCombineIntersect", action="store_true", default=False, help="Combine two tables including only common features/metadata (intersection).")
+#argp.add_argument("-e","--combineUnion", dest="fCombineUnion", action="store_true", default=False, help="Combine two tables (union).")
+
+#Dimensionality Reduction
+#argp.add_argument("-p","--doPCA", dest="fDoPCA",action="store_true", default=False, help="Flag to turn on adding metabugs and metametadata by performing PCA on each of bug relative abundance and continuous metadata and add the resulting components")
+
+#Checked
+argp.add_argument("-o","--output", dest="strOutFile", action="store", default=None, help="Indicate output pcl file.")
+argp.add_argument("strFileAbund", help ="Input data file")
+
+args = argp.parse_args( )
+
+# Creat output file if needed.
+if not args.strOutFile:
+  args.strOutFile = os.path.splitext(args.strFileAbund)[0]+"-mod.pcl"
+lsPieces = os.path.splitext(args.strOutFile)
+
+#List of abundance tables
+lsTables = []
+
+#Read in abundance table
+abndTable = AbundanceTable.funcMakeFromFile(xInputFile=args.strFileAbund,
+                                            cDelimiter = args.cFileDelimiter,
+                                            sMetadataID = args.sIDName,
+                                            sLastMetadata = args.sLastMetadataName,
+                                            lOccurenceFilter = None,
+                                            cFeatureNameDelimiter=args.cFeatureDelimiter,
+                                            xOutputFile = args.strOutFile)
+
+#TODO Check filtering, can not have some filtering together
+
+# Make feature list
+lsFeatures = []
+if args.strFeatures:
+  print "Get features not completed"
+#  if "," in args.strFeatures:
+#    lsFeatures = args.strFeatures.split(",")
+#    print "ManipulateTable::Reading in feature list "+str(len(lsFeatures))+"."
+#  else:
+#    csvr = csv.reader(open(args.strFeatures, "rU"))
+#    print "ManipulateTable::Reading in feature file "+args.strFeatures+"."
+#    for lsLine in csvr:
+#      lsFeatures.extend(lsLine)
+
+lsTables.append(abndTable)
+
+# Do summing
+#Sum if need
+if args.fSum:
+  for abndTable in lsTables:
+    print "ManipulateTable::"+abndTable.funcGetName()+" had "+str(len(abndTable.funcGetFeatureNames()))+" features before summing."
+    fResult = abndTable.funcSumClades()
+    if fResult:
+      print "ManipulateTable::"+abndTable.funcGetName()+" was summed."
+      print "ManipulateTable::"+abndTable.funcGetName()+" has "+str(len(abndTable.funcGetFeatureNames()))+" features after summing."
+    else:
+      print "ManipulateTable::ERROR. "+abndTable.funcGetName()+" was NOT summed."
+
+# Filter on counts
+if args.strFilterOccurence:
+  iMinimumSequence,iMinimumSample = args.strFilterOccurence.split(",")
+  for abndTable in lsTables:
+    if abndTable.funcIsNormalized():
+      print "ManipulateTable::ERROR. "+abndTable.funcGetName()+" is normalized and can not be filtered by occurence. This filter needs counts."
+    else:
+      fResult = abndTable.funcFilterAbundanceBySequenceOccurence(iMinSequence = int(iMinimumSequence), iMinSamples = int(iMinimumSample))
+      if fResult:
+        print "ManipulateTable::"+abndTable.funcGetName()+" was filtered by occurence and now has "+str(len(abndTable.funcGetFeatureNames()))+" features."
+      else:
+        print "ManipulateTable::ERROR. "+abndTable.funcGetName()+" was NOT filtered by occurence."
+
+# Change bug membership
+if args.fMakeTerminal:
+  lsTerminalTables = []
+  for abndTable in lsTables:
+    print "ManipulateTable::"+abndTable.funcGetName()+" had "+str(len(abndTable.funcGetFeatureNames()))+" features before making terminal."
+    abndTable = abndTable.funcGetFeatureAbundanceTable(abndTable.funcGetTerminalNodes())
+    if abndTable:
+      print "ManipulateTable::"+abndTable.funcGetName()+" has "+str(len(abndTable.funcGetFeatureNames()))+" terminal features."
+      lsTerminalTables.append(abndTable)
+    else:
+      print "ManipulateTable::ERROR. "+abndTable.funcGetName()+" was not made terminal."
+  lsTables = lsTerminalTables
+
+if args.fRemoveOTUs:
+  lsNotOTUs = []
+  for abndTable in lsTables:
+    print "ManipulateTable::"+abndTable.funcGetName()+" had "+str(len(abndTable.funcGetFeatureNames()))+" features before removing OTUs."
+    abndTable = abndTable.funcGetWithoutOTUs()
+    if abndTable:
+      print "ManipulateTable::"+abndTable.funcGetName()+" had OTUs removed and now has "+str(len(abndTable.funcGetFeatureNames()))+" features."
+      lsNotOTUs.append(abndTable)
+    else:
+      print "ManipulateTable::ERROR. "+abndTable.funcGetName()+" OTUs were not removed."
+  lsTables = lsNotOTUs
+
+if args.iClade:
+  for abndTable in lsTables:
+    fResult = abndTable.funcReduceFeaturesToCladeLevel(args.iClade)
+    if fResult:
+      print "ManipulateTable::"+abndTable.funcGetName()+" was reduced to clade level "+str(args.iClade)+"."
+    else:
+      print "ManipulateTable::ERROR. "+abndTable.funcGetName()+" was NOT reduced in clade levels."
+
+if args.strFeatures:
+  for abndTable in lsTables:
+    fResult = abndTable.funcGetFeatureAbundanceTable(lsFeatures)
+    if fResult:
+      print "ManipulateTable::"+abndTable.funcGetName()+" has been reduced to given features and now has "+str(len(abndTable.funcGetFeatureNames()))+" features."
+    else:
+      print "ManipulateTable::ERROR. "+abndTable.funcGetName()+" could not be reduced to the given list."
+
+if args.strRemoveMetadata:
+  lsMetadata = args.strRemoveMetadata.split(",")
+  for abndTable in lsTables:
+    fResult = abndTable.funcRemoveSamplesByMetadata(sMetadata=lsMetadata[0], lValuesToRemove=lsMetadata[1:])
+    if fResult:
+      print "ManipulateTable::"+abndTable.funcGetName()+" has had samples removed and now has "+str(len(abndTable.funcGetSampleNames()))+" samples."
+    else:
+      print "ManipulateTable::ERROR. Could not remove samples from "+abndTable.funcGetName()+"."
+
+# Normalize if needed
+if args.fNormalize:
+  for abndTable in lsTables:
+    fResult = abndTable.funcNormalize()
+    if fResult:
+      print "ManipulateTable::"+abndTable.funcGetName()+" was normalized."
+    else:
+      print "ManipulateTable::"+abndTable.funcGetName()+" was NOT normalized."
+
+# Filter on percentile
+if args.strFilterPercentile:
+  dPercentile,dPercentage = args.strFilterPercentile.split(",")
+  for abndTable in lsTables:
+    if abndTable.funcIsNormalized():
+      fResult = abndTable.funcFilterAbundanceByPercentile(dPercentileCutOff = float(dPercentile), dPercentageAbovePercentile = float(dPercentage))
+      if fResult:
+        print "ManipulateTable::"+abndTable.funcGetName()+" has been reduced by percentile and now has "+str(len(abndTable.funcGetFeatureNames()))+" features."
+      else:
+        print "ManipulateTable::ERROR. "+abndTable.funcGetName()+" could not be reduced by percentile."
+    else:
+      print "ManipulateTable::"+abndTable.funcGetName()+" was NOT normalized and so the percentile filter is invalid, please indicate to normalize the table."
+
+# Filter on abundance (should go after filter on percentile because the filter on percentile 
+# needs the full distribution of features in a sample
+if args.strFilterAbundance:
+  dAbundance,iMinSamples = args.strFilterAbundance.split(",")
+  dAbundance = float(dAbundance)
+  iMinSamples = int(iMinSamples)
+  for abndTable in lsTables:
+    if abndTable.funcIsNormalized():
+      fResult = abndTable.funcFilterAbundanceByMinValue(dMinAbundance=dAbundance,iMinSamples=iMinSamples)
+      if fResult:
+        print "ManipulateTable::"+abndTable.funcGetName()+" has been reduced by minimum relative abundance value and now has "+str(len(abndTable.funcGetFeatureNames()))+" features."
+      else:
+        print "ManipulateTable::ERROR. "+abndTable.funcGetName()+" could not be reduced by percentile."
+    else:
+      print "ManipulateTable::"+abndTable.funcGetName()+" was NOT normalized and so the abundance filter is invalid, please indicate to normalize the table."
+
+#if args.dCuttOff:
+#  print "Standard deviation filtering not completed"
+#  for abndTable in lsTables:
+#    abndTable.funcFilterFeatureBySD(dMinSDCuttOff=args.dCuttOff)
+#    if fResult:
+#      print "ManipulateTable::"+abndTable.funcGetName()+" has been reduced by standard deviation and now has "+str(len(abndTable.funcGetFeatureNames()))+" features."
+#    else:
+#      print "ManipulateTable::ERROR. "+abndTable.funcGetName()+" could not be reduced by standard devation."
+
+# Need to normalize again after abundance data filtering given removing features breaks the normalization
+# This happends twice because normalization is required to make the abundance data to filter on ;-)
+# Normalize if needed
+if args.fNormalize:
+  for abndTable in lsTables:
+    fResult = abndTable.funcNormalize()
+    if fResult:
+      print "ManipulateTable::"+abndTable.funcGetName()+" was normalized after filtering on abundance data."
+
+#Manipulate lineage
+if args.fPrefixClades:
+  for abndTable in lsTables:
+    fResult = abndTable.funcAddCladePrefixToFeatures()
+    if fResult:
+      print "ManipulateTable::Clade Prefix was added to "+abndTable.funcGetName()
+    else:
+      print "ManipulateTable::ERROR. Clade Prefix was NOT added to "+abndTable.funcGetName()
+
+# Under development
+# Reduce dimensionality
+#if args.fDoPCA:
+#  pcaCur = PCA()
+#  for abndTable in lsTables:
+#
+#    # Add data features
+#    # Make data components and add to abundance table
+#    pcaCur.loadData(abndTable,True)
+#    pcaCur.run(fASTransform=True)
+#    ldVariance = pcaCur.getVariance()
+#    lldComponents = pcaCur.getComponents()
+#    # Make Names
+#    lsNamesData = ["Data_PC"+str((tpleVariance[0]+1))+"_"+re.sub("[\.|-]","_",str(tpleVariance[1])) for tpleVariance in enumerate(ldVariance)]
+#    abndTable.funcAddDataFeature(lsNamesData,lldComponents)
+#
+#    # Add metadata features
+#    # Convert metadata to an input for PCA
+#    pcaCur.loadData(pcaCur.convertMetadataForPCA(abndTable),False)
+#    fSuccessful = pcaCur.run(fASTransform=False)
+#    if(fSuccessful):
+#      ldVariance = pcaCur.getVariance()
+#      lldComponents = pcaCur.getComponents()
+#      # Make Names
+#      lsNamesMetadata = ["Metadata_PC"+str((tpleVariance[0]+1))+"_"+re.sub("[\.|-]","_",str(tpleVariance[1])) for tpleVariance in enumerate(ldVariance)]
+#      # Make metadata components and add to abundance
+#      llsMetadata = [list(npdRow) for npdRow in lldComponents]
+#      abndTable.funcAddMetadataFeature(lsNamesMetadata, llsMetadata)
+#    else:
+#      print "ManipulateTable::No metadata to PCA, no PCA components added to file based on metadata"
+
+#Manipulate based on metadata
+if args.strStratifyBy:
+  labndStratifiedTables = []
+  for abndTable in lsTables:
+    labndResult = abndTable.funcStratifyByMetadata(strMetadata=args.strStratifyBy)
+    print "ManipulateTable::"+abndTable.funcGetName()+" was stratified by "+args.strStratifyBy+" in to "+str(len(labndResult))+" tables."
+    labndStratifiedTables.extend(labndResult)
+  lsTables = labndStratifiedTables
+
+if len(lsTables) == 1:
+  lsTables[0].funcWriteToFile(args.strOutFile)
+else:
+  iIndex = 1
+  for abndManTable in lsTables:
+    abndManTable.funcWriteToFile(lsPieces[0]+str(iIndex)+lsPieces[1])
+    iIndex = iIndex + 1