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main.py
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#
#
# Copyright (C) 2023 Niko Popitsch. All rights reserved.
#
# This file is part of splice_sim
#
# See the file LICENSE for redistribution information.
#
# @author: niko.popitsch@univie.ac.at
"""
Main file that does all commandline handling
"""
import json
import logging
import os
import random
import sys
from argparse import ArgumentParser, RawDescriptionHelpFormatter
from collections import OrderedDict
from splice_sim.model import Model
from splice_sim.simulator import create_genome_bam, postfilter_bam
from splice_sim.evaluator import evaluate, extract_feature_metadata, extract_bam_stats, \
special_count_HISAT3N_strand_stats, special_extract_sc_reads, filter_xc_yc_reads
VERSION = "0.1"
LOGO = """
Splice_sim v%s
""" % VERSION
def check_config(config):
for section in ['dataset_name', 'mappers', 'genome_fa', 'gene_gff', 'isoform_mode']:
assert section in config, "Missing configuration section %s" % section
if 'transcripts' not in config:
assert "transcript_data" in config, "Transcript data needs to be configured either in config file ('transcripts' section) or in an external file referenced via 'transcript_data'"
def init_logging(config, outdir):
fn = outdir + 'splice_sim.%s.log' % config['dataset_name']
print("Logging to %s" % fn)
logging.basicConfig(filename=fn, level=logging.DEBUG)
logging.info(LOGO)
usage = '''
Copyright (C) 2021 XXX. All rights reserved.
Distributed on an "AS IS" basis without warranties
or conditions of any kind, either express or implied.
USAGE
'''
if __name__ == '__main__':
parser = {}
parser["build_model"] = ArgumentParser(description=usage, formatter_class=RawDescriptionHelpFormatter)
parser["build_model"].add_argument("-c", "--config", type=str, required=True, dest="config_file",
metavar="config_file", help="JSON config file")
parser["build_model"].add_argument("-o", "--outdir", type=str, required=False, dest="outdir", metavar="outdir",
help="output directory (default is current dir)")
parser["create_genome_bam"] = ArgumentParser(description=usage, formatter_class=RawDescriptionHelpFormatter)
parser["create_genome_bam"].add_argument("-m", "--model", type=str, required=True, dest="model_file",
metavar="model_file", help="model file")
parser["create_genome_bam"].add_argument("-a", "--art_sam", type=str, required=True, dest="art_sam_file",
metavar="config_file", help="ART sam file")
parser["create_genome_bam"].add_argument("-t", "--threads", type=int, required=False, default=1, dest="threads",
metavar="threads", help="threads")
parser["create_genome_bam"].add_argument("-o", "--outdir", type=str, required=False, dest="outdir",
metavar="outdir", help="output directory (default is current dir)")
parser["postfilter_bam"] = ArgumentParser(description=usage, formatter_class=RawDescriptionHelpFormatter)
parser["postfilter_bam"].add_argument("-c", "--config", type=str, required=True, dest="config_file",
metavar="config_file", help="JSON config file")
parser["postfilter_bam"].add_argument("-b", "--bam", type=str, required=True, dest="bam_file", metavar="bam_file",
help="input bam file")
parser["postfilter_bam"].add_argument("-o", "--outdir", type=str, required=True, dest="outdir", metavar="outdir",
help="output dir")
parser["evaluate_bam_performance"] = ArgumentParser(description=usage, formatter_class=RawDescriptionHelpFormatter)
parser["evaluate_bam_performance"].add_argument("-c", "--config", type=str, required=True, dest="config_file",
metavar="config_file", help="JSON config file")
parser["evaluate_bam_performance"].add_argument("-m", "--model", type=str, required=True, dest="model_file",
metavar="model_file", help="model file")
parser["evaluate_bam_performance"].add_argument("-b", "--bam_file", type=str, required=True, dest="bam_file",
metavar="bam_file", help="input bam file")
parser["evaluate_bam_performance"].add_argument("-o", "--outdir", type=str, required=True, dest="outdir",
metavar="outdir", help="output dir")
parser["evaluate_splice_site_performance"] = ArgumentParser(description=usage,
formatter_class=RawDescriptionHelpFormatter)
parser["evaluate_splice_site_performance"].add_argument("-c", "--config", type=str, required=True,
dest="config_file", metavar="config_file",
help="JSON config file")
parser["evaluate_splice_site_performance"].add_argument("-m", "--model", type=str, required=True, dest="model_file",
metavar="model_file", help="model file")
parser["evaluate_splice_site_performance"].add_argument("-b", "--bam_file", type=str, required=True,
dest="bam_file", metavar="bam_file", help="input bam file")
parser["evaluate_splice_site_performance"].add_argument("-t", "--truth_bam_dir", type=str, required=True,
dest="truth_bam_dir", metavar="truth_bam_dir",
help="truth bam dir")
parser["evaluate_splice_site_performance"].add_argument("-o", "--outdir", type=str, required=True, dest="outdir",
metavar="outdir", help="output dir")
parser["calculate_splice_site_mappability"] = ArgumentParser(description=usage,
formatter_class=RawDescriptionHelpFormatter)
parser["calculate_splice_site_mappability"].add_argument("-c", "--config", type=str, required=True,
dest="config_file", metavar="config_file",
help="JSON config file")
parser["calculate_splice_site_mappability"].add_argument("-m", "--model", type=str, required=True,
dest="model_file", metavar="model_file", help="model file")
parser["calculate_splice_site_mappability"].add_argument("-b", "--bam_file", type=str, required=True,
dest="bam_file", metavar="bam_file", help="input bam file")
parser["calculate_splice_site_mappability"].add_argument("-t", "--truth_bam_dir", type=str, required=True,
dest="truth_bam_dir", metavar="truth_bam_dir",
help="truth bam dir")
parser["calculate_splice_site_mappability"].add_argument("-o", "--outdir", type=str, required=True, dest="outdir",
metavar="outdir", help="output dir")
parser["calc_feature_overlap"] = ArgumentParser(description=usage, formatter_class=RawDescriptionHelpFormatter)
parser["calc_feature_overlap"].add_argument("-c", "--config", type=str, required=True, dest="config_file",
metavar="config_file", help="JSON config file")
parser["calc_feature_overlap"].add_argument("-m", "--model", type=str, required=True, dest="model_file",
metavar="model_file", help="model file")
parser["calc_feature_overlap"].add_argument("-b", "--bam_file", type=str, required=True, dest="bam_file",
metavar="bam_file", help="input bam file")
parser["calc_feature_overlap"].add_argument("-o", "--outdir", type=str, required=True, dest="outdir",
metavar="outdir", help="output dir")
parser["write_parquet_db"] = ArgumentParser(description=usage, formatter_class=RawDescriptionHelpFormatter)
parser["write_parquet_db"].add_argument("-c", "--config", type=str, required=True, dest="config_file",
metavar="config_file", help="JSON config file")
parser["write_parquet_db"].add_argument("-i", "--indir", type=str, required=True, dest="indir", metavar="indir",
help="input splice_sim directory")
parser["write_parquet_db"].add_argument("-o", "--outdir", type=str, required=True, dest="outdir", metavar="outdir",
help="output dir")
parser["extract_splice_site_features"] = ArgumentParser(description=usage,
formatter_class=RawDescriptionHelpFormatter)
parser["extract_splice_site_features"].add_argument("-c", "--config", type=str, required=True, dest="config_file",
metavar="config_file", help="JSON config file")
parser["extract_splice_site_features"].add_argument("-m", "--model", type=str, required=True, dest="model_file",
metavar="model_file", help="model file")
parser["extract_splice_site_features"].add_argument("-o", "--outdir", type=str, required=True, dest="outdir",
metavar="outdir", help="output dir")
parser["extract_transcript_features"] = ArgumentParser(description=usage,
formatter_class=RawDescriptionHelpFormatter)
parser["extract_transcript_features"].add_argument("-c", "--config", type=str, required=True, dest="config_file",
metavar="config_file", help="JSON config file")
parser["extract_transcript_features"].add_argument("-m", "--model", type=str, required=True, dest="model_file",
metavar="model_file", help="model file")
parser["extract_transcript_features"].add_argument("-o", "--outdir", type=str, required=True, dest="outdir",
metavar="outdir", help="output dir")
parser["evaluate"] = ArgumentParser(description=usage, formatter_class=RawDescriptionHelpFormatter)
parser["evaluate"].add_argument("-b", "--bam_file", type=str, required=True, dest="bam_file", metavar="bam_file",
help="input bam file")
parser["evaluate"].add_argument("-c", "--config", type=str, required=True, dest="config_file",
metavar="config_file", help="JSON config file")
parser["evaluate"].add_argument("-m", "--model", type=str, required=True, dest="model_file", metavar="model_file",
help="model file")
parser["evaluate"].add_argument("-f", "--filter_bed", type=str, required=False, dest="filter_bed",
metavar="filter_bed", help="Filter regions BED file")
parser["evaluate"].add_argument("-t", "--threads", type=int, required=False, dest="threads", default=1,
help="used threads")
parser["evaluate"].add_argument("-o", "--outdir", type=str, required=True, dest="outdir", metavar="outdir",
help="output dir")
parser["extract_feature_metadata"] = ArgumentParser(description=usage, formatter_class=RawDescriptionHelpFormatter)
parser["extract_feature_metadata"].add_argument("-c", "--config", type=str, required=True, dest="config_file",
metavar="config_file", help="JSON config file")
parser["extract_feature_metadata"].add_argument("-m", "--model", type=str, required=True, dest="model_file",
metavar="model_file", help="model file")
parser["extract_feature_metadata"].add_argument("-o", "--outdir", type=str, required=True, dest="outdir",
metavar="outdir", help="output dir")
parser["extract_bam_stats"] = ArgumentParser(description=usage, formatter_class=RawDescriptionHelpFormatter)
parser["extract_bam_stats"].add_argument("-b", "--bam_file", type=str, required=True, dest="bam_file",
metavar="bam_file", help="BAM file")
parser["extract_bam_stats"].add_argument("-o", "--outdir", type=str, required=True, dest="outdir", metavar="outdir",
help="output dir")
parser["special_count_HISAT3N_strand_stats"] = ArgumentParser(description=usage,
formatter_class=RawDescriptionHelpFormatter)
parser["special_count_HISAT3N_strand_stats"].add_argument("-b", "--bam_file", type=str, required=True,
dest="bam_file", metavar="bam_file", help="BAM file")
parser["special_count_HISAT3N_strand_stats"].add_argument("-o", "--outdir", type=str, required=True, dest="outdir",
metavar="outdir", help="output dir")
parser["special_extract_sc_reads"] = ArgumentParser(description=usage, formatter_class=RawDescriptionHelpFormatter)
parser["special_extract_sc_reads"].add_argument("-b", "--bam_file", type=str, required=True, dest="bam_file",
metavar="bam_file", help="BAM file")
parser["special_extract_sc_reads"].add_argument("-r", "--region", type=str, required=True, dest="region",
metavar="region", help="BAM region")
parser["special_extract_sc_reads"].add_argument("-o", "--outdir", type=str, required=True, dest="outdir",
metavar="outdir", help="output dir")
parser["filter_xc_yc_reads"] = ArgumentParser(description=usage, formatter_class=RawDescriptionHelpFormatter)
parser["filter_xc_yc_reads"].add_argument("-b", "--bam_file", type=str, required=True, dest="bam_file",
metavar="bam_file", help="BAM file")
parser["filter_xc_yc_reads"].add_argument("-o", "--outdir", type=str, required=True, dest="outdir",
metavar="outdir", help="output dir")
# ============================================================================
if len(sys.argv) <= 1 or sys.argv[1] in ['-h', '--help']:
print("usage: splice_sim.py [-h] " + ",".join(parser.keys()))
sys.exit(1)
mod = sys.argv[1]
if mod not in parser.keys():
print("Invalid module '%s' selected. Please use one of %s" % (mod, ",".join(parser.keys())))
sys.exit(1)
args = parser[mod].parse_args(sys.argv[2:])
# ============================================================================
# output dir (current dir if none provided)
outdir = os.path.abspath(args.outdir if args.outdir else os.getcwd()) + '/'
if not os.path.exists(outdir):
os.makedirs(outdir)
if mod == "build_model":
# load and check onfig
config = json.load(open(args.config_file), object_pairs_hook=OrderedDict)
init_logging(config, outdir)
check_config(config)
Model.build_model(args.config_file, outdir)
if mod == "create_genome_bam":
# load model
m = Model.load_from_file(args.model_file)
config = m.config
init_logging(config, outdir)
# set random seed
if "random_seed" in config:
random.seed(config["random_seed"])
logging.info("setting random seed to %i" % config["random_seed"])
create_genome_bam(m, args.art_sam_file, args.threads, outdir)
if mod == "postfilter_bam":
config = json.load(open(args.config_file), object_pairs_hook=OrderedDict)
init_logging(config, outdir)
postfilter_bam(config, args.bam_file, outdir)
if mod == "evaluate":
# load config to be able to react to config changes after model was built!
config = json.load(open(args.config_file), object_pairs_hook=OrderedDict)
init_logging(config, outdir)
print("load model")
m = Model.load_from_file(args.model_file)
print("evaluate")
# set random seed
if "random_seed" in config:
random.seed(config["random_seed"])
logging.info("setting random seed to %i" % config["random_seed"])
evaluate(config, m, args.bam_file, args.filter_bed, args.threads, outdir)
if mod == "extract_feature_metadata":
# load config to be able to react to config changes after model was built!
config = json.load(open(args.config_file), object_pairs_hook=OrderedDict)
init_logging(config, outdir)
print("load model")
m = Model.load_from_file(args.model_file)
print("extract_feature_metadata")
# set random seed
if "random_seed" in config:
random.seed(config["random_seed"])
logging.info("setting random seed to %i" % config["random_seed"])
extract_feature_metadata(config, m, outdir)
if mod == "extract_bam_stats":
print("extract_bam_stats")
extract_bam_stats(args.bam_file, outdir)
if mod == "special_count_HISAT3N_strand_stats":
print("special_count_HISAT3N_strand_stats")
special_count_HISAT3N_strand_stats(args.bam_file, outdir)
if mod == "special_extract_sc_reads":
print("special_extract_sc_reads")
special_extract_sc_reads(args.bam_file, args.region, outdir)
if mod == "filter_xc_yc_reads":
print("filter_xc_yc_reads")
filter_xc_yc_reads(args.bam_file, outdir)