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xombo.py
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xombo.py
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########################################################################
########################################################################
"""
xombo.py
Description: Xombo - An XNA toolkit. Manages scripts for integrating
various ONT processing pipelines required for signal extraction and
signal alignment of raw nanopore reads.
Title: Synthesis and Sequencing of a 12-Letter Supernumerary DNA
By: H. Kawabe, C. Thomas, S. Hoshika, Myong-Jung Kim, Myong-Sang Kim, L. Miessner, J. M. Craig,
J. Gundlach, A. Laszlo, S. A. Benner, J. A. Marchand
Updated: 2/14/23
"""
########################################################################
########################################################################
import argparse, textwrap
import os
import sys
parser = argparse.ArgumentParser(
usage='"python xombo.py [-h] {split, basecall, subset, preprocess, resquiggle, get-level}',
formatter_class=argparse.RawTextHelpFormatter,
description= textwrap.dedent('''
********** Xombo *********
Xombo is a suite of tools built from Tombo to streamline processing and level extraction of fast5 files.
Xombo command groups (additional help available within each command group):
split Split multi-fast5 into single fast5 format and merge directory
basecall Basecall single fast5 directory using guppy
subset Subset a portion of single fast5 files to a new directory
preprocess Add fastq basecalls to single fast5 files
resquiggle Resquiggle single fast5 files using Tombo
plot-motif Plot resquiggle aligned to reference mapping using Tombo
get-level Get mean levels of resquiggled data centered around desired 4-kmer
'''))
subparsers = parser.add_subparsers(dest='subparsers')
parser_split = subparsers.add_parser('split', help='[fast5_dir] [output_dir]')
parser_split.add_argument('fast5_dir',metavar ='[fast5_dir]', type=str, help='Input directory containing multi-fast5 folders.')
parser_split.add_argument('output_dir', metavar ='[output_dir]', type=str, help='Output directory for storing single-fast5 files')
parser_basecall = subparsers.add_parser('basecall', help='[single_fast5_dir] [fastq_output_dir]')
parser_basecall.add_argument('fast5_dir',metavar ='[fast5_dir]', type=str, help='Input directory containing multi-fast5 folders.')
parser_basecall.add_argument('output_dir', metavar ='[output_dir]', type=str, help='Output directory for storing fastq files')
parser_basecall.add_argument('-r',metavar = '[ref_fasta]', type=str, required = False, help='Basecall using a reference fasta file')
parser_subset = subparsers.add_parser('subset', help='[fast5_dir] [output_dir] [n]')
parser_subset.add_argument('fast5_dir', metavar = '[fast5_dir]', type=str, help='Input directory containing single-fast5 files.')
parser_subset.add_argument('output_dir', metavar = '[output_dir]', type=str, help='Directory to move copy of fast5 files. ')
parser_subset.add_argument('n_files', metavar = '[n]', type=int, help='Number of files to move to new directory.')
parser_preprocess = subparsers.add_parser('preprocess', help='[fast5_dir] [fastq_dir]')
parser_preprocess.add_argument('fast5_dir',metavar = '[fast5_dir]', type=str, help='Input directory containing single-fast5 files.')
parser_preprocess.add_argument('fastq_dir',metavar = '[fastq_dir]', type=str, help='Input directory containing fastq basecall files.')
parser_resquiggle = subparsers.add_parser('resquiggle', help='[fast5_dir] [fasta_ref]')
parser_resquiggle.add_argument('fast5_dir',metavar = '[fast5_dir]', type=str, help='Input directory containing basecalled single-fast5 files.')
parser_resquiggle.add_argument('fasta_ref',metavar = '[fasta_ref]', type=str, help='Fasta reference file for mapping.')
parser_resquiggle.add_argument('-g',metavar = '[raw_corr_group]', type=str, required = False, help='Raw corrected group name for storing resquiggle index. Default RawGenomeCorrected_000.')
parser_preprocess = subparsers.add_parser('plot-motif', help='[fast5_dir] [fasta_ref] -m [motif]')
parser_preprocess.add_argument('fast5_dir',metavar = '[fast5_dir]', type=str, help='Input directory containing resquiggled single-fast5 files.')
parser_preprocess.add_argument('fasta_ref',metavar = '[fasta_ref]', type=str, help='Fasta reference file for mapping.')
parser_preprocess.add_argument('-w',metavar = '[window_size]', type=str, help='Window size of base pairs to plot (default = 50)')
parser_preprocess.add_argument('-r',metavar = '[num_regions]', type=str, help='Number of regions to plot (default = 25)')
parser_preprocess.add_argument('-o',metavar = '[output_file]', type=str, help='Output file name e.g. dir/file.pdf. Default plots/tombo_results.motif_centered.pdf')
parser_preprocess = subparsers.add_parser('get-level', help='[fast5_dir] [fasta_ref] [kmer_params]')
parser_preprocess.add_argument('fast5_dir',metavar = '[fast5_dir]', type=str, help='Input directory containing resquiggled single-fast5 files.')
parser_preprocess.add_argument('fasta_ref',metavar = '[fasta_ref]', type=str, help='Fasta reference file for mapping.')
parser_preprocess.add_argument('kmer_params',metavar = '[kmer_params]', type=str, help='File containing parameters for kmer extraction and processing.')
parser_preprocess.add_argument('-o',metavar = '[output_file]', type=str, help='Output file name e.g. dir/levels.csv.')
args = parser.parse_args()
args.subparsers
#Print help if no arguments provided
if args.subparsers==None:
parser.print_help()
sys.exit(0)
#Parse arguments
if args.subparsers == 'split' :
os.system('python lib/split.py '+args.fast5_dir+' '+args.output_dir)
elif args.subparsers == 'basecall' and args.r:
os.system('python lib/basecall.py '+args.fast5_dir+' '+args.output_dir+' '+args.r)
elif args.subparsers == 'basecall' and not args.r:
os.system('python lib/basecall.py '+args.fast5_dir+' '+args.output_dir)
elif args.subparsers == 'subset':
os.system('python lib/subset.py '+args.fast5_dir+' '+args.output_dir+' '+str(args.n_files))
elif args.subparsers == 'preprocess':
os.system('python lib/preprocess.py '+args.fast5_dir+' '+args.fastq_dir)
elif args.subparsers == 'resquiggle':
raw_group = ''
if args.g:
raw_group = args.g
os.system('python lib/resquiggle.py '+args.fast5_dir+' '+args.fasta_ref+' '+raw_group)