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(" ")