--- a/cpo_galaxy_prediction.py	Mon Aug 27 19:58:24 2018 -0400
+++ b/cpo_galaxy_prediction.py	Tue Aug 28 15:15:09 2018 -0400
@@ -42,6 +42,7 @@
     parser.add_option("-e", "--expected", dest="expectedSpecies", default="NA/NA/NA", type="string", help="expected species of the isolate")
     parser.add_option("-s", "--mlst-scheme", dest="mlstScheme", default= "./scheme_species_map.tab", type="string", help="absolute file path to mlst scheme")
     parser.add_option("-p", "--plasmidfinder", dest="plasmidfinder", type="string", help="absolute file path to plasmidfinder ")
+    parser.add_options("-d", "--mash", dest="mash", type="string", help="absolute file path to mash plasmiddb result")
 
     #parallelization, useless, these are hard coded to 8cores/64G RAM
     #parser.add_option("-t", "--threads", dest="threads", default=8, type="int", help="number of cpu to use")
@@ -60,6 +61,7 @@
     expectedSpecies = str(options.expectedSpecies).lstrip().rstrip()
     mlstScheme = str(options.mlstScheme).lstrip().rstrip()
     plasmidfinder = str(options.plasmidfinder).lstrip().rstrip()
+    mash = str(options.mash).lstrip().rstrip()
     outputDir = "./"
     print(mlst)
     print(mobfindercontig)
@@ -68,6 +70,8 @@
     print(rgi)
     print(expectedSpecies)
     print(mlstScheme)
+    print(mash)
+
 else:
     curDir = os.getcwd()
     ID = "BC11"
@@ -79,6 +83,7 @@
     expectedSpecies = "Escherichia coli"
     mlstScheme = "D:\OneDrive\ProjectCDC\ProjectCDCInPython\ProjectCDCInPython\pipelineTest\scheme_species_map.tab"
     plasmidfinder = "D:\OneDrive\ProjectCDC\ProjectCDCInPython\ProjectCDCInPython\pipelineTest\predictions\BC11-Kpn005_S2.origins"
+    mash = "D:\OneDrive\ProjectCDC\ProjectCDCInPython\ProjectCDCInPython\pipelineTest\predictions\mash.tsv"
     outputDir = "./"
 
 #region result objects
@@ -190,6 +195,26 @@
         self.source = ""
         self.row = ""
 
+class MashResult(object):
+    def __init__(self):
+        self.size = 0.0
+        self.depth = 0.0
+        self.identity = 0.0
+        self.sharedHashes = ""
+        self.medianMultiplicity = 0
+        self.pvalue = 0.0
+        self.queryID= ""
+        self.queryComment = ""
+        self.species = ""
+        self.row = ""
+        self.accession = ""
+        self.gcf=""
+        self.assembly=""
+
+    def toDict(self): #doesnt actually work
+        return dict((name, getattr(self, name)) for name in dir(self) if not name.startswith('__')) 
+
+
 #endregion
 
 #region useful functions
@@ -476,6 +501,22 @@
         #plasmidFinderContigs.append(str(plasmidFinder.iloc[i,1]))
         #origins.append(str(plasmidFinder.iloc[i,4][:plasmidFinder.iloc[i,4].index("_")]))
     return _pFinder
+
+def ParseMashResult(pathToMashScreen):
+    mashScreen = pandas.read_csv(pathToMashScreen, delimiter='\t', header=None)
+
+    _mashPlasmidHits = {} #***********************
+    #parse what the species are.
+    for i in (range(len(mashScreen.index))):
+        mr = MashResult()
+        mr.identity = float(mashScreen.ix[i, 0])
+        mr.sharedHashes = mashScreen.ix[i, 1]
+        mr.medianMultiplicity = int(mashScreen.ix[i, 2])
+        mr.pvalue = float(mashScreen.ix[i, 3])
+        mr.name = mashScreen.ix[i, 4] #accession
+        mr.row = "\t".join(str(x) for x in mashScreen.ix[i].tolist())
+        _mashPlasmidHits[mr.name] = mr
+    return _mashPlasmidHits
 #endregion
 
 def Main():
@@ -531,6 +572,9 @@
     rgiAMR = ParseRGIResult(rgi, plasmidContigs, likelyPlasmidContigs) # outputDir + "/predictions/" + ID + ".rgi.txt", plasmidContigs, likelyPlasmidContigs)#***********************
     ToJson(rgiAMR, "rgi.json") #*************
 
+    plasmidFamily = ParseMashResult(mash)
+    ToJson(plasmidFamily, "mash.json")
+
     carbapenamases = [] 
     resfinderCarbas = [] #list of rfinder objects for lindaout list
     amrGenes = []
@@ -613,20 +657,27 @@
     lindaTemp += "\t\t" #sero and kcap
     
     #resfinderCarbas
+    index = 0
     for carbs in resfinderCarbas:
         if (carbs.source == "plasmid"): #
-            lindaTemp += "\t\t\t\t\t" #plasmid 1 rflp plasmid 1 family information. PLASMID_1_FAMILY\tPLASMID_1_BEST_MATCH\tPLASMID_1_COVERAGE\tPLASMID_1_SNVS_TO_BEST_MATCH
+            lindaTemp += "\t"
+            plasmid = plasmidFamily[list(plasmidFamily.keys())[index]]
+            lindaTemp += plasmid.name + "\t"
+            lindaTemp += str(plasmid.identity) + "\t"
+            lindaTemp += plasmid.sharedHashes + "\t"
             lindaTemp += carbs.shortGene + "\t" #found an carbapenase
             contig = carbs.sequence[6:] #this is the contig number
             for i in mSuite.keys():
                 if (str(mSuite[i].contig_num) == str(contig)): #found the right plasmid
-                    lindaTemp += mSuite[i].rep_type
+                    clusterid = mSuite[i].cluster_id
+                    rep_types = mSuitePlasmids["plasmid_" + str(clusterid) + ".fasta"].rep_types
+                    lindaTemp += rep_types
     lindaOut.append(lindaTemp)
     out = open("summary.linda.tsv", 'w')
     for item in lindaOut:
         out.write("%s\n" % item)
 
-    tsvOut.append("new\tID\tExpected Species\tMLST Species\tSequence Type\tMLST Scheme\tCarbapenem Resistance Genes\tOther AMR Genes\tTotal Plasmids\tPlasmids ID\tNum_Contigs\tPlasmid Length\tPlasmid RepType\tPlasmid Mobility\tNearest Reference\tDefinitely Plasmid Contigs\tLikely Plasmid Contigs")
+    tsvOut.append("new\tID\tExpected Species\tMLST Species\tSequence Type\tMLST Scheme\tCarbapenem Resistance Genes\tOther AMR Genes\tPlasmid Best Match\tTotal Plasmids\tPlasmids ID\tNum_Contigs\tPlasmid Length\tPlasmid RepType\tPlasmid Mobility\tNearest Reference\tDefinitely Plasmid Contigs\tLikely Plasmid Contigs")
     #start with ID
     temp = "\t"
     temp += (ID + "\t")
@@ -642,6 +693,7 @@
     temp += ";".join(amrGenes) + "\t"
 
     #lastly plasmids
+    temp += str(plasmidFamily[list(plasmidFamily.keys())[0]].name)
     temp+= str(len(mSuitePlasmids)) + "\t"
     plasmidID = ""
     contigs = ""

--- a/cpo_galaxy_predictions.xml	Mon Aug 27 19:58:24 2018 -0400
+++ b/cpo_galaxy_predictions.xml	Tue Aug 28 15:15:09 2018 -0400
@@ -11,11 +11,12 @@
 		'-m $mlst'
 		'-c $mobsuitecontig'
 		'-f $mobsuiteaggregate'
-		'-a $abricate'
+		'-a $resfinder'
 		'-r $rgi'
 		'-e $expected'
 		'-s $__tool_directory__/scheme_species_map.tab'
     '-p $plasmidfinder'
+    '-d $mash'
     ]]>
 	</command>
     <inputs>
@@ -23,15 +24,16 @@
         <param type="data" name="mlst" format="tabular" />
         <param type="data" name="mobsuitecontig" format="tabular" />
         <param type="data" name="mobsuiteaggregate" format="tabular" />
-        <param type="data" name="abricate" format="tabular" />
+        <param type="data" name="resfinder" format="tabular" />
         <param type="data" name="rgi" format="tabular" />
         <param type="data" name="plasmidfinder" format="tabular" />
+        <param type="data" name="mash" format ="tabular"/>
         <param type="text" name="expected" optional ="false"/>
     </inputs>
     <outputs>
         <data name="tsvSummary" format="tabular" from_work_dir="summary.tsv"/>
-          <data name="tsvSummaryExistingFormat" format="tabular" from_work_dir="summary.linda.tsv"/>
-		  <data name="txtSummary" format="txt" from_work_dir="summary.txt"/>
+        <data name="tsvSummaryExistingFormat" format="tabular" from_work_dir="summary.linda.tsv"/>
+		    <data name="txtSummary" format="txt" from_work_dir="summary.txt"/>
     </outputs>
 	<tests>
         <test>

--- a/cpo_galaxy_tree.py	Mon Aug 27 19:58:24 2018 -0400
+++ b/cpo_galaxy_tree.py	Tue Aug 28 15:15:09 2018 -0400
@@ -39,18 +39,53 @@
 
 #parses some parameters
 parser = optparse.OptionParser("Usage: %prog [options] arg1 arg2 ...")
-parser.add_option("-t", "--tree", dest="treePath", type="string", default="./pipelineTest/tree.txt", help="identifier of the isolate")    
-parser.add_option("-d", "--distance", dest="distancePath", type="string", default="./pipelineTest/distance.tab", help="absolute file path forward read (R1)")
-parser.add_option("-m", "--metadata", dest="metadataPath", type="string", default="./pipelineTest/metadata.tsv",help="absolute file path to reverse read (R2)")
+parser.add_option("-t", "--tree", dest="treePath", type="string", default="./pipelineTest/tree.txt", help="absolute file path to phylip tree")    
+parser.add_option("-d", "--distance", dest="distancePath", type="string", default="./pipelineTest/distance.tab", help="absolute file path to distance matrix")
+parser.add_option("-m", "--metadata", dest="metadataPath", type="string", default="./pipelineTest/metadata.tsv",help="absolute file path to metadata file")
+parser.add_option("-o", "--output_file", dest="outputFile", type="string", default="tree.png", help="Output graphics file. Use ending 'png', 'pdf' or 'svg' to specify file format.")
+
+# sensitive data adder
+parser.add_option("-p", "--sensitive_data", dest="sensitivePath", type="string", default="", help="Spreadsheet (CSV) with sensitive metadata")
+parser.add_option("-c", "--sensitive_cols", dest="sensitiveCols", type="string", default="", help="CSV list of column names from sensitive metadata spreadsheet to use as labels on dendrogram")
+parser.add_option("-b", "--bcid_column", dest="bcidCol", type="string", default="BCID", help="Column name of BCID in sensitive metadata file")
+parser.add_option("-n", "--missing_value", dest="naValue", type="string", default="NA", help="Value to write for missing data.")
+
 (options,args) = parser.parse_args()
 treePath = str(options.treePath).lstrip().rstrip()
 distancePath = str(options.distancePath).lstrip().rstrip()
 metadataPath = str(options.metadataPath).lstrip().rstrip()
 
+sensitivePath = str(options.sensitivePath).lstrip().rstrip()
+sensitiveCols = str(options.sensitiveCols).lstrip().rstrip()
+outputFile = str(options.outputFile).lstrip().rstrip()
+bcidCol = str( str(options.bcidCol).lstrip().rstrip() ) 
+naValue = str( str(options.naValue).lstrip().rstrip() ) 
+
 
 #region result objects
 #define some objects to store values from results
 #//TODO this is not the proper way of get/set private object variables. every value has manually assigned defaults intead of specified in init(). Also, use property(def getVar, def setVar).
+
+class SensitiveMetadata(object):
+    def __init__(self):
+        x = pandas.read_csv( sensitivePath )
+        col_names = [ s for s in sensitiveCols.split(',')] # convert to 0 offset
+        if not bcidCol in col_names:
+            col_names.append( bcidCol )
+        all_cols = [ str(col) for col in x.columns ]
+        col_idxs = [ all_cols.index(col) for col in col_names ]
+        self.sensitive_data = x.iloc[:, col_idxs]
+    def get_columns(self):
+        cols = [ str(x) for x in self.sensitive_data.columns ]
+        return cols
+    def get_value( self, bcid, column_name ): # might be nice to get them all in single call via an input list of bcids ... for later
+        bcids= list( self.sensitive_data.loc[:, bcidCol ] ) # get the list of all BCIDs  in sensitive metadata
+        if not bcid in bcids:
+            return naValue
+        else:
+            row_idx = bcids.index( bcid )                        # lookup the row for this BCID
+        return self.sensitive_data.loc[ row_idx, column_name ]  # return the one value based on the column (col_idx) and this row
+
 class workflowResult(object):
     def __init__(self):
         self.new = False
@@ -60,6 +95,7 @@
         self.SequenceType = "?"
         self.MLSTScheme = "?"
         self.CarbapenemResistanceGenes ="?"
+        self.plasmidBestMatch ="?"
         self.OtherAMRGenes="?"
         self.TotalPlasmids = -1
         self.plasmids = []
@@ -145,6 +181,7 @@
         _results.CarbapenemResistanceGenes = (str(r.loc[r.index[i], 'Carbapenem Resistance Genes']))
         _results.OtherAMRGenes = (str(r.loc[r.index[i], 'Other AMR Genes']))
         _results.TotalPlasmids = int(r.loc[r.index[i], 'Total Plasmids'])
+        _results.plasmidBestMatch = str(r.loc[r.index[i], 'Plasmid Best Match'])
         for j in range(0,_results.TotalPlasmids):
             _plasmid = plasmidObj()
             _plasmid.PlasmidsID =(((str(r.loc[r.index[i], 'Plasmids ID'])).split(";"))[j])
@@ -163,6 +200,9 @@
 #endregion
 
 def Main():
+    if len(sensitivePath)>0:
+        sensitive_meta_data = SensitiveMetadata()
+
     metadata = ParseWorkflowResults(metadataPath)
     distance = read(distancePath)
     treeFile = "".join(read(treePath))
@@ -212,6 +252,12 @@
         if (n.is_leaf() and n.name == "Reference"):
             #if its the reference branch, populate the faces with column headers
             index = 0
+
+            if len(sensitivePath)>0: #sensitive metadat @ chris
+                for sensitive_data_column in sensitive_meta_data.get_columns():
+                    (t&"Reference").add_face(addFace(sensitive_data_column), index, "aligned")
+                    index = index + 1
+
             (t&"Reference").add_face(addFace("SampleID"), index, "aligned")
             index = index + 1
             (t&"Reference").add_face(addFace("New?"), index, "aligned")
@@ -225,12 +271,28 @@
             index = index + 1 
             (t&"Reference").add_face(addFace("Carbapenamases"), index, "aligned")
             index = index + 1
+            (t&"Reference").add_face(addFace("Plasmid Best Match"), index, "aligned")
+            index = index + 1
             for i in range(len(distanceDict[list(distanceDict.keys())[0]])): #this loop adds the distance matrix
                 (t&"Reference").add_face(addFace(distanceDict[list(distanceDict.keys())[0]][i]), index + i, "aligned")
             index = index + len(distanceDict[list(distanceDict.keys())[0]])
         elif (n.is_leaf() and not n.name == "Reference"): 
             #not reference branches, populate with metadata
             index = 0
+
+            if len(sensitivePath)>0: #sensitive metadata @ chris
+                # pushing in sensitive data
+                for sensitive_data_column in sensitive_meta_data.get_columns():
+                    # tree uses bcids like BC18A021A_S12
+                    # while sens meta-data uses BC18A021A
+                    # trim the "_S.*" if present
+                    bcid = str(mData.ID)
+                    if bcid.find( "_S" ) != -1:
+                        bcid = bcid[ 0:bcid.find( "_S" ) ]
+                    sens_col_val = sensitive_meta_data.get_value(bcid=bcid, column_name=sensitive_data_column )
+                    n.add_face(addFace(sens_col_val), index, "aligned")
+                    index = index + 1
+
             if (n.name.replace(".fa","") in metadata.keys()):
                 mData = metadata[n.name.replace(".fa","")]
             else:
@@ -262,11 +324,13 @@
             index = index + 1
             n.add_face(addFace(mData.CarbapenemResistanceGenes), index, "aligned")
             index = index + 1
+            n.add_face(addFace(mData.plasmidBestMatch), index, "aligned")
+            index = index + 1
             for i in range(len(distanceDict[list(distanceDict.keys())[0]])): #this loop adds distance matrix
                 if (n.name in distanceDict): #make sure the column is in the distance matrice
                     n.add_face(addFace(list(distanceDict[n.name])[i]), index + i, "aligned")
                 
-    t.render("./tree.pdf", w=5000,units="mm", tree_style=ts) #save it as a png. or an phyloxml
+    t.render(outputFile, w=5000,units="mm", tree_style=ts) #save it as a png, pdf, svg or an phyloxml
 
     #endregion
 #endregion

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpo_mash.xml	Tue Aug 28 15:15:09 2018 -0400
@@ -0,0 +1,31 @@
+<tool id="cpo_clustalw" name="cpo_clustalw" version="2.1">
+  <description>Modified version of mash 2.0 with custom database</description>
+  <requirements>
+     <requirement type="package" version="2.0">mash</requirement>
+  </requirements>   
+  <command detect_errors="exit_code">
+  <![CDATA[  
+    mash screen $__tool_directory__/bcPlasmidDB.msh $input | sort -gr | head -10 > mashresult.tsv 
+  ]]>  
+  </command>
+  <inputs>
+    <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
+  </inputs>
+  <outputs>
+    <data name="mashResult" format="tabular" from_work_dir="mashresult.tsv"/> 
+  </outputs>
+  <help>
+    mash screen bcPlasmidDB.msh $input | sort -gr | head -10 > mashresult.tsv
+  </help>
+  <citations>
+    <citation type="bibtex">
+  @misc{githubmob-suite,
+  author = {Robertson J, Nash J},
+  title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  doi = {10.1099/mgen.0.000206},
+  url = {https://github.com/phac-nml/mob-suite}
+    }</citation>
+  </citations>
+</tool>
\ No newline at end of file