<commit_before>#author: <NAME>, <EMAIL>

'''
Assemble trimmed Illumina read files (fastq)
'''

import os
import sys
import re
import glob
import shutil
import argparse
import commands
import subprocess

#XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
#%%% Input %%%

# Complete path function
class CompletePath(argparse.Action):
        """give the full path of an input file/folder"""
        def __call__(self, parser, namespace, values, option_string=None):
		setattr(namespace, self.dest, os.path.abspath(os.path.expanduser(values)))


def add_arguments(parser):
        parser.add_argument(
		'--input',
		required=True,
		action=CompletePath,
		default=None,
		help='Call the folder that contains the trimmed reads, organized in a separate subfolder for each sample. The name of the subfolder has to start with the sample name, delimited with an underscore [_]'
	)
	parser.add_argument(
		'--output',
		required=True,
		action=CompletePath,
		default=None,
		help='The output directory where results will be safed'
	)
	parser.add_argument(
		'--assembler',
		choices=["trinity", "abyss"],
		default="abyss",
		help="""The assembler to use."""
	)
        '''
	parser.add_argument(
		'--trinity',
		default="/usr/local/bin/trinityrnaseq_r20140717/Trinity",
		action=CompletePath,
		help='The path to the Trinity executable'
	)
	parser.add_argument(
		'--abyss',
		default="/usr/local/packages/anaconda2/bin/abyss-pe",
		action=CompletePath,
		help='The path to the abyss-pe executable'
	)<commit_msg>Fixing small typos<commit_after>#author: <NAME>, <EMAIL>

'''
Assemble trimmed Illumina read files (fastq)
'''

import os
import sys
import re
import glob
import shutil
import argparse
import commands
import subprocess

#XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
#%%% Input %%%

# Complete path function
class CompletePath(argparse.Action):
        """give the full path of an input file/folder"""
        def __call__(self, parser, namespace, values, option_string=None):
		setattr(namespace, self.dest, os.path.abspath(os.path.expanduser(values)))


def add_arguments(parser):
        parser.add_argument(
		'--input',
		required=True,
		action=CompletePath,
		default=None,
		help='Call the folder that contains the trimmed reads, organized in a separate subfolder for each sample. The name of the subfolder has to start with the sample name, delimited with an underscore [_]'
	)
	parser.add_argument(
		'--output',
		required=True,
		action=CompletePath,
		default=None,
		help='The output directory where results will be saved'
	)
	parser.add_argument(
		'--assembler',
		choices=["trinity", "abyss"],
		default="abyss",
		help="""The assembler to use."""
	)
        '''
	parser.add_argument(
		'--trinity',
		default="/usr/local/bin/trinityrnaseq_r20140717/Trinity",
		action=CompletePath,
		help='The path to the Trinity executable'
	)
	parser.add_argument(
		'--abyss',
		default="/usr/local/packages/anaconda2/bin/abyss-pe",
		action=CompletePath,
		help='The path to the abyss-pe executable'
	)
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{'dir': 'git-commits-cleaned', 'id': '5596764', 'n_tokens_mistral': 1060, 'n_tokens_neox': 976, 'n_words': 262}