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#! /usr/bin/env python3
"""Dump per-read statistics
This script takes a per-read statistics file and dumps its contents out into a tab-separated values file. The columns in the file are 'chrm', 'pos', 'strand', 'read_id' and 'stat'.
"""
from tombo import tombo_stats
from tombo.tombo_helper import intervalData
import argparse
import sys
import os
def extract_per_read_stats(input_file, output_file):
"""Dump per-read statistics to tab-separated values"""
if not os.path.isfile(input_file):
sys.exit('"{}" is not a valid file'.format(input_file))
pr_stats = tombo_stats.PerReadStats(input_file)
with open(output_file, 'w') as out_fp:
out_fp.write('{}\t{}\t{}\t{}\t{}\n'.format(
'chrm', 'pos', 'strand', 'read_id', 'stat'))
for (chrm, strand), cs_blocks in list(pr_stats.blocks_index.items()):
for start, block_name in list(cs_blocks.items()):
for pos, stat, read_id in pr_stats.get_region_per_read_stats(
intervalData(chrm, start, start + pr_stats.region_size,
strand)):
out_fp.write('{}\t{}\t{}\t{}\t{}\n'.format(
chrm, pos, strand, read_id, stat))
def main(input_file, output_file):
extract_per_read_stats(input_file, output_file)
if __name__ == '__main__':
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument(
'input_file',
type=str,
help="the per-read statistics file produced by tombo"
)
parser.add_argument(
'-o',
'--output_file',
default='per_read_stats.txt',
type=str,
help="the name of the output tsv file (default: 'per_read_stats.txt')"
)
args = parser.parse_args()
main(args.input_file, args.output_file)
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