--- a
+++ b/src/combine.py
@@ -0,0 +1,62 @@
+import csv
+from glob import glob
+import re
+
+FILES = glob("F:/NYU/Hackathon/**/*.mirna.quantification.txt")
+print FILES.count
+FILES.sort()
+#print FILES
+OUT_FILE = 'F:/NYU/Hackathon/output_file'
+
+output_writer = open(OUT_FILE, 'a')
+
+patients = dict()
+id = 0
+
+for file in FILES:
+	print "processing file ", file
+	output_writer.write("\n")
+
+	m = re.search("TCGA-..-([A-Za-z0-9]{4,4})-(\d{2,2})[A-Za-z]", file)
+	#print m
+	patient_id = m.group(1)
+	tissue_type = m.group(2)
+	
+	if patient_id not in patients:
+		id = id + 1
+		patients[patient_id] = id;
+
+	patient_id = patients[patient_id]
+
+	cancer_type = 2
+	tmp = re.search("PAAD", file)
+	if tmp is not None:
+		cancer_type = 1
+
+	output_writer.write("{0} {1} {2} ".format(patient_id, cancer_type, tissue_type))
+	with open(file, 'r') as myFile:
+		reader = csv.reader(myFile, delimiter='\t')
+		count = 0
+		for row in reader:
+			try:
+				if count == 0:
+					count += 1
+					continue
+				
+				#has_header = csv.Sniffer().has_header(myFile.read(1024))
+				#reads_per_million_miRNA_mapped = 'NA'
+				#myFile.seek(0)  # rewind
+				#incsv = csv.reader(myFile)
+				#if has_header:
+				#	next(incsv)  # skip header row
+				reads_per_million_miRNA_mapped = row[2]
+				if reads_per_million_miRNA_mapped == 'NA':
+					reads_per_million_miRNA_mapped = '0.0'
+				reads_per_million_miRNA_mapped = float(reads_per_million_miRNA_mapped)
+				output_writer.write(str(reads_per_million_miRNA_mapped))
+				
+			except ValueError as e:
+				output_writer.write('0.0')
+				print "Exception wile reading line ", reader.line_num, " from file ", file, "  Expeced a float. Got ", reads_per_million_miRNA_mapped
+			
+			output_writer.write(" ")
\ No newline at end of file