--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/ConstantsMicropita.py	Tue May 13 21:58:57 2014 -0400
@@ -0,0 +1,208 @@
+"""
+Author: Timothy Tickle
+Description: Constants.
+"""
+
+#####################################################################################
+#Copyright (C) <2012>
+#
+#Permission is hereby granted, free of charge, to any person obtaining a copy of
+#this software and associated documentation files (the "Software"), to deal in the
+#Software without restriction, including without limitation the rights to use, copy,
+#modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
+#and to permit persons to whom the Software is furnished to do so, subject to
+#the following conditions:
+#
+#The above copyright notice and this permission notice shall be included in all copies
+#or substantial portions of the Software.
+#
+#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+#INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+#PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+#OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+#SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#####################################################################################
+
+__author__ = "Timothy Tickle"
+__copyright__ = "Copyright 2012"
+__credits__ = ["Timothy Tickle"]
+__license__ = "MIT"
+__maintainer__ = "Timothy Tickle"
+__email__ = "ttickle@sph.harvard.edu"
+__status__ = "Development"
+
+from breadcrumbs.src.Metric import Metric
+
+class ConstantsMicropita():
+    """
+    Class to hold project constants.
+    """
+
+    #Character Constants
+    COLON = ":"
+    COMMA = ","
+    FASTA_ID_LINE_START = ">"
+    QUOTE = "\""
+    TAB = '\t'
+    WHITE_SPACE = " "
+    PIPE = "|"
+    c_outputFileDelim = '\t'
+
+    c_sEmptyPredictFileValue = 'NA'
+
+    #Used to stop divide by zero errors
+    c_smallNumber = 0.00000000001
+
+    #SVM related
+    c_COST_RANGE_KEY = "range"
+    c_lCostRange = [-5,-4,-3,-2,-1,0,1,2,3,4,5,6,7,8,9,10]
+    c_SCALED_FILE_EXT = ".scaled"
+    c_intScaleLowerBound = 0
+    #LIBSVM file extensions
+    c_SCALING_PARAMETERS = ".range"
+    c_CV_FILE_EXT = ".cv.out"
+    c_CV_IMAGE_EXT = ".cv.png"
+    c_MODEL_FILE_EXT = ".model"
+    c_PREDICT_FILE_EXT = ".predict"
+    c_fProbabilitistic = True
+    c_SCALED_FOR_PREDICTION_FILE_EXT = ".scaledForpredict"
+
+    #SVM output Dictionary keywords for files
+    c_strKeywordInputFile = "INPUT"
+    c_strKeywordScaledFile = "SCALED"
+    c_strKeywordRangeFile = "RANGE"
+    c_strKeywordCVOutFile = "CV_OUT"
+    c_strKeywordModelFile = "MODEL"
+    c_strKeywordScaledPredFile = "SCALED_FOR_PREDICTION"
+    c_strKeywordPredFile = "PREDICTION"
+    c_strKeywordCostValue = "C"
+    c_strKeywordAccuracy = "ACCURACY"
+
+    #Default values for missing data in the Abundance Table
+    c_strEmptyAbundanceData = "0"
+    c_strEmptyDataMetadata = "NA"
+    lNAs = list(set(["NA","na","Na","nA",c_strEmptyDataMetadata]))
+
+    #Occurence filter [min abundance, min samples occuring in]
+    #To turn off make == [0,0]
+    c_liOccurenceFilter = [0,0]
+
+    #Break ties in targeted feature with diversity
+    c_fBreakRankTiesByDiversity = False
+
+    ####Commandline arguments
+    #a Custom diversity metrics found in cogent
+    c_strCustomAlphaDiversityHelp = "A key word for any PyCogent supplied alpha diveristy metric (Richness, evenness, or diversity). Please supply an unnormalized (counts) abundance table for these metrics. Metrics include "+" ".join(Metric.setAlphaDiversities)+"."
+
+    #b Custom diversity metrics found in cogent
+    c_strCustomBetaDiversityHelp = "A key word for any PyCogent supplied beta diversity metric. Metrics include "+" ".join(list(Metric.setBetaDiversities)+[Metric.c_strUnifracUnweighted,Metric.c_strUnifracWeighted])+"."
+
+    #c,checked Checked abundance file
+    c_strCheckedAbundanceFileArgument = "--checked"
+    c_strCheckedAbundanceFileHelp = "Before analysis abundance files are checked and a new file results which analysis is perfromed on. The name of the checked file can be specified of the default will will be used (appending a -Checked to the end of the file name)."
+
+    #d,id Name of the sample id row
+    c_strIDNameArgument = "--id"
+    c_strIDNameHelp = "The row in the abundance file that is the sample name/id row. Should be the sample name/Id in first column of the row."
+
+    #e,label Supervised Label
+    c_strSupervisedLabelArgument = "--label"
+    c_strSupervisedLabelHelp = "The name of the metadata on which to perform supervised methods"
+
+    #f, invertDiversity
+    c_strInvertDiversityHelp = "".join(["When using this flag, the diversity will be inverted (multiplicative inverse) before ranking in the highest diversity method. ",
+			       "Recommended to use with dominance, menhinick, reciprocal_simpson, berger_parker_d, mcintosh_e, simpson_e, strong and any metric where 0 indicates most diverse."])
+
+    #g,logging Path of the logging file
+    c_strLoggingFileArgument = "--logfile"
+    c_strLoggingFileHelp = "File path to save the logging file."
+
+    #h help
+
+    #i,tree
+    c_strCustomEnvironmentFileHelp = "File describing the smaple environments; for use with Unifrac distance metrics."
+
+    #j,delim File delimiter
+    c_strFileDelimiterArgument = "--delim"
+    c_strFileDelimiterHelp = "The delimiter for the abundance table (default = TAB)"
+
+    #k,featdelim Feature delimiter
+    c_strFeatureNameDelimiterArgument = "--featdelim"
+    c_strFeatureNameDelimiterHelp = "The delimiter for a feature name if it contains a consensus sequence."
+
+    #l,lastmeta The name of the last metadata
+    c_strLastMetadataNameArgument = "--lastmeta"
+    c_strLastMetadataNameHelp = "The row in the abundance file that is the sample name/id row. Should be the metadata name/Id in first column of the metadta row."
+
+    #m,method
+    c_strSelectionTechniquesHelp = "Select techniques listed one after another."
+
+    #n,num The Number of unsupervised sample selection
+    c_strCountArgument = "-n"
+    c_strCountHelp = "The number of samples to select with unsupervised methodology. (An integer greater than 0.)."
+
+    #o,tree
+    c_strCustomPhylogeneticTreeHelp = "Tree for phylogenetic when selecting custom beta-diversities in the representative sampling criteria."
+
+    #p,suppredfile File path fo the predict file for the supervised methods
+    c_strSupervisedPredictedFile = "--suppredfile"
+    c_strSupervisedPredictedFileHelp = "The file path for the predict file."
+
+    #q,alphameta
+    c_strCustomAlphaDiversityMetadataHelp = "Metric in the pcl file which has custom alpha diversity measurements to use with the highest diversity sampling criteria. Should be a number between 0.0 and 1.0 with 1.0 meaning most diverse."
+
+    #r,targetmethod Taxa selection method
+    c_strTargetedFeatureMethodArgument = "--feature_method"
+    c_strTargetedFeatureMethodHelp = "The ranking method used to select targeted features."
+
+    #s,stratify Unsupervised stratify metadata
+    c_strUnsupervisedStratifyMetadataArgument = "--stratify"
+    c_strUnsupervisedStratifyMetadataHelp = "The metatdata to stratify unsupervised analysis."
+
+    #t,target Targeted feature file
+    c_strTargetedSelectionFileArgument = "--targets"
+    c_strTargetedSelectionFileHelp = "A file containing taxa/OTUs/clades to be used in targeted feature sampling criteria."
+
+    #u,supinputfile File path for the input file for the supervised methods
+    c_strSupervisedInputFile = "--supinputfile"
+    c_strSupervisedInputFileHelp = "The file path for the input file for supervised methods."
+
+    #v,logging String for logging level
+    c_strLoggingArgument = "--logging"
+    c_strLoggingHelp = "".join(["Logging level which will be logged to a .log file with the",
+         " same name as the strOutFile (but with a .log extension). Valid values are DEBUG, INFO, WARNING, ERROR, or CRITICAL."])
+    c_lsLoggingChoices = ["DEBUG","INFO","WARNING","ERROR","CRITICAL"]
+
+    #w, Last Feature Metadata indicator
+    c_strFeatureMetadataArgument = "--lastFeatureMetadata"
+    c_strFeatureMetadataHelp = "The last metadata describing a (bug) feature (not sample). Not all studies have feature metadata, if so this can be ignored and not used. See doc for PCL-Description.txt"
+
+    #x,betamatrix
+    c_strCustomBetaDiversityMatrixHelp = "Precalculated beta-diversity matrix to be used in the representative sampling criteria. Should be a number between 0.0 and 1.0 with 1.0 meaning most dissimilar."
+
+    #Order is important, the first is the default
+    c_strTargetedRanked = "rank"
+    c_strTargetedAbundance = "abundance"
+    lsTargetedFeatureMethodValues = [c_strTargetedRanked, c_strTargetedAbundance]
+
+    #Selection methods
+    c_strDiversity = "diverse"
+    c_strExtreme = "extreme"
+    c_strDiscriminant = "discriminant"
+    c_strDistinct = "distinct"
+    c_strRandom = "random"
+    c_strRepresentative = "representative"
+    c_strFeature = "features"
+    c_custom = "custom"
+    c_lsAllUnsupervisedMethods = [c_strRepresentative,c_strDiversity,c_strExtreme,c_strFeature,c_strRandom]
+    c_lsAllSupervisedMethods = [c_strDiscriminant,c_strDistinct]
+    c_lsAllMethods = c_lsAllUnsupervisedMethods + c_lsAllSupervisedMethods
+
+    #Technique Names
+    c_strDiversity2 = c_strDiversity+"_C"
+
+    ####################################
+    #Arguments without commandline flags
+    c_strAbundanceFileHelp = "Input file as either a PCL or Biome file."
+    c_strGenericOutputDataFileHelp = "The generated output data file."