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enrichmenTE_input.py
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enrichmenTE_input.py
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#!/usr/bin/env python3
import argparse
import os
def get_args():
parser = argparse.ArgumentParser(
description="""
Software to detect non-reference TEs from TE-NGS data
enrichmenTE consists of two major steps:
- DETECT detects non-reference insertions for five TE families: 1731,297,copia,mdg1,roo
- CLUSTER cluster samples based on TE profiles of five TE families
"""
)
subparsers = parser.add_subparsers(help="modes", dest="sub")
parser_detect = subparsers.add_parser(
"detect",
help="Detect TE insertions using TE-NGS data",
)
## required ##
parser_detect.add_argument(
"-1",
"--read1",
type=str,
help="read 1 fastq.gz file or file list",
required=True,
)
parser_detect.add_argument(
"-2",
"--read2",
type=str,
help="read 2 fastq.gz file or file list",
required=True,
)
parser_detect.add_argument(
"-r",
"--reference",
type=str,
help="masked augmented reference genome",
required=True,
)
parser_detect.add_argument(
"-f",
"--filter_region",
type=str,
help="filter out region in bed format",
required=True,
)
parser_detect.add_argument(
"-g",
"--gff",
type=str,
help="reference TE annotation in bed file",
required=True,
)
parser_detect.add_argument(
"-d",
"--depth_config",
type=str,
help="depth cutoff config file for identifying TE clusters",
required=True,
)
## optional
parser_detect.add_argument(
"-p",
"--prefix",
help="Prefix for output files",
required=False,
)
parser_detect.add_argument(
"-w",
"--window",
type=int,
help="merge window for identifying TE clusters (default = 100bp) ",
required=False,
)
parser_detect.add_argument(
"--tsd_max", type=int, help="maximum TSD size (default = 25) ", required=False
)
parser_detect.add_argument(
"--gap_max", type=int, help="maximum gap size (default = 25) ", required=False
)
parser_detect.add_argument(
"-t", "--thread", type=int, help="thread (default = 1) ", required=False
)
parser_detect.add_argument(
"-o", "--out", type=str, help="output dir (default = '.') ", required=False
)
# parameters for cluster module
parser_cluster = subparsers.add_parser(
"cluster",
help="Cluster samples based on TE profile",
)
parser_cluster.add_argument(
"--prefix",
type=str,
help="output prefix",
required=True,
)
parser_cluster.add_argument(
"--enrichmente_out_dirs",
type=str,
help="list of enrichmenTE output directories",
nargs="+",
required=True,
)
parser_cluster.add_argument(
"--filter_region",
type=str,
help="filter region in bed format, separated by comma",
required=True,
)
parser_cluster.add_argument("--outgroup", type=str, help="outgroup", required=False)
parser_cluster.add_argument(
"-o",
"--out",
type=str,
help="directory to output results)",
required=True,
)
parser_cluster.add_argument(
"--include_families",
type=str,
help="TE families to use in the phylogeny (separated by comma)",
required=False,
)
parser_cluster.add_argument(
"--exclude_families",
type=str,
help="TE families to exclude in the phylogeny (separated by comma)",
required=False,
)
parser_cluster.add_argument(
"--exclude_samples",
type=str,
help="sample to exclude in the phylogeny (separated by comma)",
required=False,
)
parser_cluster.add_argument(
"--thread",
type=int,
help="max cpu threads to use (default = '1')",
required=False,
)
args = parser.parse_args()
# sets up out dir variable
if args.out is None:
args.out = "."
args.out = os.path.abspath(args.out)
if not os.path.exists(args.out):
os.mkdir(args.out)
return args