<commit_before>#!/usr/bin/env python 
"""
Program to run transcriptome assembly using TransriptSkimmer on read alignment data 

Requirement: 
    TransriptSkimmer - 

"""

import os 
import subprocess

def run_trsk(org_name, gio_file, bam_file, res_path, gff_file="pred_genes.gff", reg_file="pred_region.bed"):
    """
    run TransriptSkimmer for provided genome


    """

    res_path = "%s/%s/trans_pred/" % (res_path, org_name)

    max_exon_length = org_db
    max_intron_length = org_db
    max_intergenic_region = org_db

    options="-maxel %d -ss -reglen 0.66 -maxic %d -minic 20 -maxin %d -mm 2 -exm 3 -indt 150 -exd 20 -tf 0.5 -inscf 3 -excut 3 -toff 100 -el 15" % (max_exon_length, max_intergenic_region, max_intron_length)


    os.chdir(res_path) 

    gio_file = org_db
    trsk_path = org_db

    cli = "%s./infer_genes -gio %s -bam %s -gff %s -reg %s %s" % (trsk_path, gio_file, bam_file, gff_file, reg_file, options)  
    sys.stdout.write('\trun %s \n' % cli)

    process = subprocess.Popen(cli, shell=True) 
    process.wait()
<commit_msg>fixing the options for TSKM<commit_after>#!/usr/bin/env python 
"""
Program to run transcriptome assembly using TransriptSkimmer on read alignment data 

Requirement: 
    TransriptSkimmer - 

"""

import os 
import subprocess

def run_trsk(org_name, gio_file, bam_file, res_path, gff_file="pred_genes.gff", reg_file="pred_region.bed"):
    """
    run TransriptSkimmer for provided genome

    """

    res_path = "%s/%s/trans_pred/" % (res_path, org_name)

    max_exon_length = 
    max_intron_length = 
    max_intergenic_region = 

    options="-maxel %d -ss -reglen 0.66 -maxic %d -minic 20 -maxin %d -mm 2 -exm 3 -indt 150 -exd 20 -tf 0.5 -inscf 3 -excut 3 -toff 100 -el 15" % (max_exon_length, max_intergenic_region, max_intron_length)

    os.chdir(res_path) 

    gio_file = 
    trsk_path = 

    cli = "%s./infer_genes -gio %s -bam %s -gff %s -reg %s %s" % (trsk_path, gio_file, bam_file, gff_file, reg_file, options)  
    sys.stdout.write('\trun %s \n' % cli)

    process = subprocess.Popen(cli, shell=True) 
    process.wait()

{'fraction_non_alphanumeric': 0.12167300380228137, 'fraction_numerical': 0.019961977186311788, 'mean_word_length': 3.2525252525252526, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, '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': '5272850', 'n_tokens_mistral': 896, 'n_tokens_neox': 804, 'n_words': 205}