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generate_sequence_list.py
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generate_sequence_list.py
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#!/bin/env python
'''
generate_sequence_list.py
Copyright (c) 2015, David Edwards, Bernie Pope, Kat Holt
All rights reserved. (see README.txt for more details)
Run if there is no 'sequence_list.txt' available.
Requires the '*_AllStats_user.txt' file be available in the
output folder.
example:
python generate_sequence_list.py <RedDog_output_folder>
Created: 12/03/2014
Modified:
author: David Edwards
'''
import sys, glob
from pipe_utils import splitPath
output_folder_name = sys.argv[1]
if output_folder_name[-1] != '/':
output_folder_name += '/'
user_file_name = output_folder_name + '*_AllStats_user.txt'
file_names = []
file_names = glob.glob(user_file_name)
if len(file_names) > 1:
print "Too many AllStats_user.txt file found in " + output_folder
sys.exit()
elif len(file_names) < 1:
print "No AllStats_user.txt file found in " + output_folder
sys.exit()
user_file = open(file_names[0], 'r')
sequence_list = user_file.readline()
user_file.close()
sequences = sequence_list.split()
output = ''
for item in range(1, len(sequences)):
output += sequences[item] + '\n'
output_folder_name += 'sequence_list.txt'
output_file = open(output_folder_name, 'w')
output_file.write(output)
output_file.close()