import os
import glob
import shutil
import re

# Python 2.7.11 written by Ali Khalighifar on July 14, 2017
# This script seperates each replicate from the outputs of EstimateS and creates a new table (text file) of them.
baseDir = 'Working Directory'
finalDir = baseDir + '\Dest_result'
os.chdir(baseDir)
if (not(os.path.isdir(finalDir))):
    os.mkdir(finalDir)
# Splitting each replicate of EstimateS outputs by finding the beginning of the replicate
start_split = 'EstimateS (Version 9.1.0), Copyright R. K. Colwell:  http://purl.oclc.org/estimates\nDiversity Output from Input File:  '
txtFiles = [txt_file for txt_file in glob.iglob ('*.txt')]
a = 1
for output in txtFiles:
    result = open (output, 'U')
    lines = result.read()
    split_up = lines.split(start_split)
    del split_up[0]
    print len(split_up)
    first = str.split(output, '.txt')
    filenames = first[0]
    filenames = re.findall(r'\d{1,4}_days', filenames)
    filenames = filenames[0]
    filenames = filenames.replace('_', '')
    print filenames
    for i,name in enumerate(split_up):
        # "nine" is the code for the error abundance and "High" is the code for the mean abundance of real Species
        f = open('nine'+'High'+filenames+'Rep'+str(i+a)+'.txt','w')
        f.write(name+'\n')
        f.close()
        source = baseDir+'\\'+'nine'+'High'+filenames+'Rep'+str(i+a)+'.txt'
        dest = finalDir + '\\' +'nine'+'High'+filenames
        if (not(os.path.isdir(dest))):
           os.mkdir(dest) 
        shutil.move(source, dest)