diff cpo_galaxy_tree.py @ 18:596bf8a792de draft

planemo upload

--- 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