<commit_before># -*- coding: utf-8 -*-
import sys, traceback
import os
import shutil
import requests
import time
import grequests
import itertools
from itertools import product
import multiprocessing as mp
from multiprocessing import Pool
import logging
import subprocess
from subprocess import check_call
import codecs
from xml.etree import ElementTree as ET

argvs = sys.argv
argc = len(argvs)

sailfish_dname = '/data/sailfish_index'
sailfish_0_9_dname = '/data/sailfish_0.9_index'
bowtie2_dname = '/data/bowtie2_index'
tophat_dname = '/data/tophat_index'
hisat2_dname = '/data/hisat2_index'
loc_dname = '/galaxy-central/tool-data'

if (argc != 4):
    print 'Usage: # python %s index_list_mrna index_list_tophat2 index_list_hisat2' % argvs[0]
    quit()

def read_input(args):
    f = open(argvs[args])
    ret_list = []

    for i in f.readlines():
        i = i.strip()
        if len(i) < 1:
            continue
        ret_list = ret_list + [i]

    f.close
    return ret_list

def create_loc_file(index_list, loc_name, dirname):
    f = codecs.open(loc_name, "w", "utf-8")
    for item in index_list:
        index_id = item.split(',')[0]
        index_name = item.split(',')[1]
        
        if "sailfish" in dirname or "hisat2" in dirname:<commit_msg>modefied HISAT2 index.loc wrong path<commit_after># -*- coding: utf-8 -*-
import sys, traceback
import os
import shutil
import requests
import time
import grequests
import itertools
from itertools import product
import multiprocessing as mp
from multiprocessing import Pool
import logging
import subprocess
from subprocess import check_call
import codecs
from xml.etree import ElementTree as ET

argvs = sys.argv
argc = len(argvs)

sailfish_dname = '/data/sailfish_index'
sailfish_0_9_dname = '/data/sailfish_0.9_index'
bowtie2_dname = '/data/bowtie2_index'
tophat_dname = '/data/tophat_index'
hisat2_dname = '/data/hisat2_index'
loc_dname = '/galaxy-central/tool-data'

if (argc != 4):
    print 'Usage: # python %s index_list_mrna index_list_tophat2 index_list_hisat2' % argvs[0]
    quit()

def read_input(args):
    f = open(argvs[args])
    ret_list = []

    for i in f.readlines():
        i = i.strip()
        if len(i) < 1:
            continue
        ret_list = ret_list + [i]

    f.close
    return ret_list

def create_loc_file(index_list, loc_name, dirname):
    f = codecs.open(loc_name, "w", "utf-8")
    for item in index_list:
        index_id = item.split(',')[0]
        index_name = item.split(',')[1]
        
        if "sailfish" in dirname:
{'fraction_non_alphanumeric': 0.10615627466456196, 'fraction_numerical': 0.014206787687450671, 'mean_word_length': 3.478798586572438, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2347993', 'n_tokens_mistral': 929, 'n_tokens_neox': 915, 'n_words': 237}