def run_trinity(bam_files, output_dir, log_dir, num_cores, max_intron,
jaccard_clip_flag):
D_conf = import_config(this_dir)
trinity_bin = D_conf['TRINITY_PATH']
# Trinity --genome_guided_bam rnaseq_alignments.csorted.bam
# --max_memory 50G --genome_guided_max_intron 2000 --CPU 6
for bam_file in bam_files:
prefix = (os.path.splitext(os.path.basename(bam_file))[0])
outdir = os.path.join(output_dir, 'trinity_{}'.format(prefix))
new_output = os.path.join(outdir, 'Trinity_{}.fasta'.format(prefix))
logger_time.debug('START: Trinity for {}'.format(prefix))
if not os.path.exists(new_output):
log_file = os.path.join(log_dir, program_name,
'trinity_{}.log'.format(prefix))
command = (
'{} {} --genome_guided_bam {} --genome_guided_max_intron {} '
'--max_memory {} --CPU {} --output {} > {} 2>&1'.format(
trinity_bin, jaccard_clip_flag, bam_file, max_intron,
max_memory, num_cores, outdir, log_file))
logger_txt.debug('[Run] {}'.format(command))
os.system(command)
# Rename the file
trinity_output = os.path.join(outdir, 'Trinity-GG.fasta')
os.rename(trinity_output, new_output)
else:
logger_txt.debug(
'Running Trinity has already been finished {}'.format(prefix))
logger_time.debug('DONE : Trinity for {}'.format(prefix))
def check_busco_dataset(busco_dataset):
'''Check BUSCO dataset'''
d_conf = import_config()
busco_bin = d_conf['BUSCO_PATH']
proc = subprocess.Popen([busco_bin, '--list-datasets'],
stdout=subprocess.PIPE)
output = str(proc.stdout.read().decode('utf-8'))
busco_dbs = re.findall(r'\S+_odb10', output)
if busco_dataset not in set(busco_dbs):
sys.exit(
'[ERROR] Invalid BUSCO DATASET: {}. Run busco --list-datasets to '
'get a full list available datasets'.format(busco_dataset))
print('BUSCO_DATASET is ok...')
def run_repeat_modeler(genome_assembly, output_dir, log_dir, num_cores):
D_conf = import_config(this_dir)
builddatabase_bin = D_conf['BUILDDATABASE_PATH']
repeatmodeler_bin = D_conf['REPEATMODELER_PATH']
# BuildDatabase -name Choanephora_cucurbitarum
# ../Choanephora_cucurbitarum_assembly.fna
# RepeatModeler -database Choanephora_cucurbitarum -pa 25
# Get repeat model
repeat_lib = os.path.join(
output_dir, '*', 'consensi.fa.classified'
)
if not glob(repeat_lib):
os.chdir(os.path.join(output_dir))
logger_time.debug('START running RepeatModeler')
log_file1 = os.path.join(
log_dir, program_name, 'build_database.log'
)
command1 = '{} -name {} {} > {} 2>&1'.format(
builddatabase_bin, genome_assembly, genome_assembly, log_file1
)
logger_txt.debug('[Run] {}'.format(command1))
os.system(command1)
log_file2 = os.path.join(
log_dir, program_name, 'repeat_modeler.log'
)
command2 = '{} -database {} -pa {} > {} 2>&1'.format(
repeatmodeler_bin, genome_assembly, num_cores, log_file2
)
logger_txt.debug('[Run] {}'.format(command2))
os.system(command2)
logger_time.debug('DONE running RepeatModeler')
else:
logger_txt.debug('Running RepeatModeler has already been finished')
# Check if RepeatModeler is properly finished
if not glob(repeat_lib):
logger_txt.debug(
'[ERROR] RepeatModeler has finished abnormally. There is no '
'consensi.fa.classified file.'
)
sys.exit(2)
Input: FASTQ files and genome assembly
Output: SAM and converted BAM file using SAMtools.
Last updated: Jul 13, 2020
'''
import os
import re
import sys
from argparse import ArgumentParser
from import_config import import_config
from set_logging import set_logging
# Parameters
D_CONF = import_config()
# Main function
def main():
'''Main function'''
argparser_usage = (
'run_hisat2.py -r <fastq1> <fastq2> <fastq3> ...'
' -o <output_dir> -l <log_dir> -f <ref_fasta> -c <num_cores>'
' -m <max_intron>'
)
parser = ArgumentParser(usage=argparser_usage)
parser.add_argument(
'-r', '--read_files', nargs='+', required=True,
help='Multiople read files in fastq format'
)
from Bio.Alphabet import IUPAC
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
from collections import defaultdict
from argparse import ArgumentParser
from Bio.Alphabet import generic_dna
# Get Logging
this_path = os.path.realpath(__file__)
this_dir = os.path.dirname(this_path)
sys.path.append(this_dir)
from import_config import import_config
# Parameters
D_conf = import_config(this_dir)
# Main function
def main(argv):
argparse_usage = (
'create_markdown.py -f <input_fasta> -g <input_gff3> '
'-t <trinity_assembly> -b <bam_file> -o <output_dir>'
)
parser = ArgumentParser(usage=argparse_usage)
parser.add_argument(
'-f', '--input_fasta', nargs=1, required=True,
help='Genome assembly file in FASTA format'
)
parser.add_argument(
'-g', '--input_gff3', nargs=1, required=True,
from export_files import export_files
from process_files import process_files
from import_config import import_config
opt = '10'
while int(opt) not in [0, 1, 2, 3, 4]:
print("[1] Import Configurations")
print("[2] Process Files")
print("[3] Export File")
print("[0] Exit")
opt = input("Choose 1 to 4: ")
if opt == '1':
im = import_config()
im.import_config()
elif opt == '2':
pr = process_files()
pr.process_files()
elif opt == '3':
ex = export_files()
ex.export_file()
elif opt == '0':
print("Goodbye!")
exit(0)
