#!/usr/bin/env python

# This code is to concatenate the batch GO Term Finder results (.tsv) generated from batch GTF perl code(Chris Johnson, U of Tulsa) into a list table

import sys, os, string, glob


# return the file list
def list_all_files(Path):
    list_all_files = []
    list_all_files = glob.glob(Path +'/*.txt.tsv')
    return list_all_files


# Main function

try:
   data_file_Path = sys.argv[1]
   output_file_Path = sys.argv[2]
except: 
   print 'Usage: python Concatenate_GTF_results.py /datasetPath /outputFilePath_and_Name'
   print 'Data file not found, error in given directory'
   sys.exit(1)

# Open the output file

try:
    output = open(output_file_Path, 'w')
except OSError:
    print 'output file error'

# get all the GTF result files in given directory
File_list = []
File_list = list_all_files(data_file_Path)
File_list.sort()

i = 0
for file in File_list:
    #parse the file names given in absolute path
    file_name = file.strip().split('/')[-1]
    file_name = file_name.rstrip('.txt.tsv')
    # function to read tsv files from a given directory
    #open the file
    data = open(file,'r')
    #reading the label line
    labelLine = data.readline()
    label = labelLine.strip().split('\t')
    #write the label
    #updates2010July26: update following label writing code	
    if i == 0:
    #    output.write('cluster origin')
        for element in label:
            output.write(element)
            output.write('\t')
    i = i + 1
    #updates2010July26 End
    #switch to the next line
    output.write('\n')

    #read the GO terms
    GOTermLines = data.readlines()
    for GOTerm in GOTermLines:
        GOTerm = GOTerm.strip().strip('\t')
        if GOTerm != '':
	    #updates2010July26: remove the code to write the first column 'REMc cluster ID'
            #output.write(file_name)
            #output.write('\t')
	    ##updates2010July26 update end
            output.write(GOTerm + '\n')
            #output.write('\n')
output.close()