Merge branch 'master' of github.com:sh1992/OrangeWidgets

BioinformaticFileWidget/BF.py

@@ -0,0 +1,172 @@
+#bioinformatic file management functions to be implemented
+
+#goals
+    #take multiple files and merge them into single data table
+    #be able to transpose matrix(switching from samples to genes as entries)
+    #be able to deal with FASTA formats(WHY DOESNT ORANGE DO THIS?)
+
+"""
+IMPORTS
+"""
+import os
+import sys
+import csv
+
+"""
+GLOBALS
+"""
+EXAMPLEFILELIST=['breast-cancer-wisconsin.tab', 'breast-cancer-wisconsin-cont.tab']
+
+
+"""
+SCRIPT
+"""
+
+#fasta reader
+def fastaReader(fastaFile):
+
+    pass
+
+
+
+def transposeMatrix(textfile):  #what structure to use for matrix? array?  npArray?  nested lists?
+    file = open(textfile, 'r')
+    file2 = open(textfile, 'w')
+    for c in zip(*(l.split() for l in file.readlines() if l.strip())):
+        file2.write(' '.join(c))
+    return file2
+
+
+def concatFiles(path): #should arguments be directory
+
+    #initialize dictionary
+    dataDict = {}
+
+    #get list of files
+    fileList = os.listdir(path)
+
+    #for each file in file list
+    for f in fileList:
+
+        #open file
+        fh = open(os.path.join(path,f),'r')
+
+        #skip header
+        header = fh.readline()
+
+        #grab first line
+        firstLine = fh.readline().strip("\n").split("\t")
+
+        #intialize dictionary for paitient by paitient id
+        dataDict[firstLine[0]] = {}
+
+        #add first gene from first line
+        dataDict[firstLine[0]][firstLine[1]] = firstLine[2]
+
+        #for rest of lines
+        for i in fh.readlines():
+            line = i.strip("\n").split("\t")
+            dataDict[line[0]][line[1]] = line[2]
+
+    return dataDict
+
+
+def makeDataFile(newFileName,dataDict):
+	fh = open(newFileName,'w')
+	paitients = dataDict.keys()
+	genes = dataDict[paitients[0]].keys()
+
+	header = "patientID\t"
+	for g in genes:
+		header += g
+		header += "\t"
+	header += "value\n"
+
+	fh.write(header)
+
+	shitz = "d\t"
+	for i in range(len(genes)):
+		shitz += "c\t"
+	shitz += "\n"
+
+	fh.write(shitz)
+
+	for p in patients:
+		line = p
+		line += "\t"
+		for g in genes:
+			line += dataDict[p][g]
+			line += "\t"
+		line += "\n"
+		fh.write(line)
+	fh.close
+
+def makeCSVDataFile(newFileName,dataDict):
+	fh = open(newFileName,'w')
+	writer = csv.writer(fh,delimiter = "\t")
+	patients = dataDict.keys()
+	genes = dataDict[patients[0]].keys()
+
+	header = []
+	header.append("patientID")
+	for g in genes:
+		header.append(g)
+	header.append('value')
+
+	writer.writerow(header)
+
+	for p in patients:
+		line = []
+		line.append(p)
+		for g in genes:
+			line.append(dataDict[p][g])
+		writer.writerow(line)
+
+	fh.close
+
+
+
+
+def concat(flist, column_overlap=0, transpose=False):
+  """
+  A concatonate function that returns a large data table of 
+  the files in flist.
+
+  Assumes that all files are properly aligned.  Will terminate
+  in error if file lengths do not line up appropriately.
+
+  column_overlap specifies the number of repeat columns 
+  in the files.  Ignores these columns from concatonation.
+
+  Transpose calls the transpose function before returning the 
+  data file matrix.
+
+  returns a numpy array of all file constituents.
+  """
+
+  data = []       #Container for all file data desired
+
+  for num, fil in enumerate(flist):
+    f = open(fil, 'r')
+    reader = csv.reader(f, delimiter='\t')  #init csv reader on each file in list
+
+    line_i = reader.next()
+    i = 0   #counter to make sure which line we are on.
+    if num < 1:  #if it is the first file, add straight to data
+      while line_i:
+        data.append(line_i)   #add to data as new list
+        try:
+          line_i = reader.next()
+        except:
+          break  #exit loop gracefully.
+    else: # all other files after first...
+      while line_i:
+        data[i].extend(line_i[column_overlap:])  # .. extend the i-th list in data
+        try:
+          line_i = reader.next()
+          i += 1   #update the counter
+        except:
+          break    #end gracefully
+
+  return data  #may addd as numpy array later, if desired.
+

BioinformaticFileWidget/BFW.py

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+#bioinformatic file widget to be implemented
+import BF		#this is where the functions for dealing with stuff go
+import sys
+sys.path.append("C:\\Python27\\Lib\\site-packages\\Orange\\OrangeWidgets")
+from OWWidget import *
+import OWGUI
+import numpy as np
+
+class Bio-file(OWWidget):
+
+    def __init__(self, parent=None, signalManager=None):
+        OWWidget.__init__(self, parent, signalManager, 'Bio-File')
+
+        #self.inputs = [("Data", ExampleTable, self.data)]
+        self.outputs = [("Sampled Data", ExampleTable)]
+
+        # GUI
+        box = OWGUI.widgetBox(self.controlArea, "Info")
+        self.infoa = OWGUI.widgetLabel(box, 'File tool to help import, organize, and manipulate data of various file types from within orange.')
+        self.infob = OWGUI.widgetLabel(box, '')
+        self.resize(100,50)
+
+
+#goals
+	#take multiple files and merge them into single data table
+	#be able to transpose matrix(switching from samples to genes as entries)
+	#be able to deal with FASTA formats(WHY DOESNT ORANGE DO THIS?)
+
+
+