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#!/usr/bin/env python
Counts reads.
__author__ = "Nathan Sheffield"
__email__ = ""
__license__ = "GPL3"
__version__ = "0.1"
from argparse import ArgumentParser
import os, re
import sys
import subprocess
import yaml
import pypiper
parser = ArgumentParser(
description="A pipeline to count the number of reads and file size. Accepts"
" BAM, fastq, or fastq.gz files.")
# First, add standard arguments from Pypiper.
# groups="pypiper" will add all the arguments that pypiper uses,
# and adding "common" adds arguments for --input and --sample--name
# and "output_parent". You can read more about your options for standard
# arguments in the pypiper docs (section "command-line arguments")
parser = pypiper.add_pypiper_args(parser, groups=["pypiper", "common", "ngs"],
args=["output-parent", "config"],
required=['sample-name', 'output-parent'])
# Add any pipeline-specific arguments if you like here.
args = parser.parse_args()
if not args.input or not args.output_parent:
raise SystemExit
if args.single_or_paired == "paired":
args.paired_end = True
args.paired_end = False
# args for `output_parent` and `sample_name` were added by the standard
# `add_pypiper_args` function.
# A good practice is to make an output folder for each sample, housed under
# the parent output folder, like this:
outfolder = os.path.abspath(os.path.join(args.output_parent, args.sample_name))
# Create a PipelineManager object and start the pipeline
pm = pypiper.PipelineManager(name="count",
# NGSTk is a "toolkit" that comes with pypiper, providing some functions
# for dealing with genome sequence data. You can read more about toolkits in the
# documentation
# Create a ngstk object
ngstk = pypiper.NGSTk(pm=pm)
raw_folder = os.path.join(outfolder, "raw/")
fastq_folder = os.path.join(outfolder, "fastq/")
# Merge/Link sample input and Fastq conversion
# These commands merge (if multiple) or link (if single) input files,
# then convert (if necessary, for bam, fastq, or gz format) files to fastq.
# We'll start with a timestamp that will provide a division for this section
# in the log file
pm.timestamp("### Merge/link and fastq conversion: ")
# Now we'll rely on 2 NGSTk functions that can handle inputs of various types
# and convert these to fastq files.
local_input_files = ngstk.merge_or_link(
[args.input, args.input2],
cmd, out_fastq_pre, unaligned_fastq = ngstk.input_to_fastq(
# Now we'll use another NGSTk function to grab the file size from the input files
pm.report_result("File_mb", ngstk.get_file_size(local_input_files))
# And then count the number of reads in the file
n_input_files = len(list(filter(bool, local_input_files)))
raw_reads = sum([int(ngstk.count_reads(input_file, args.paired_end))
for input_file in local_input_files]) / n_input_files
# Finally, we use the report_result() function to print the output and
# log the key-value pair in the standard stats.tsv file
pm.report_result("Raw_reads", str(raw_reads))
# Cleanup