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#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2013-2015, Michigan State University.
# Copyright (C) 2015, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
#
# * Neither the name of the Michigan State University nor the names
# of its contributors may be used to endorse or promote products
# derived from this software without specific prior written
# permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project@idyll.org
# pylint: disable=missing-docstring
"""
Display summary statistics for one or more FASTA/FASTQ files.
% scripts/readstats.py [ -o output.txt ] <file1> <file2>
Use '-h' for parameter help.
"""
from __future__ import print_function
import argparse
import sys
import csv
import screed
import textwrap
from khmer.khmer_args import sanitize_help, KhmerArgumentParser
def get_parser():
descr = "Display summary statistics for one or more FASTA/FASTQ files."
epilog = """\
Report number of bases, number of sequences, and average sequence length
for one or more FASTA/FASTQ files; and report aggregate statistics at end.
With :option:`-o`/:option:`--output`, the output will be saved to the
specified file.
Example::
readstats.py tests/test-data/test-abund-read-2.fa
"""
parser = KhmerArgumentParser(
description=descr,
epilog=textwrap.dedent(epilog))
parser.add_argument('filenames', nargs='+')
parser.add_argument('-o', '--output', dest='outfp', metavar="filename",
help="output file for statistics; defaults to stdout.",
type=argparse.FileType('w'), default=sys.stdout)
parser.add_argument('--csv', default=False, action='store_true',
help='Use the CSV format for the statistics, '
'including column headers.')
return parser
class StatisticsOutput(object): # pylint: disable=too-few-public-methods
"""
Output statistics for several data files.
The format of the output is determined by the formatter used.
All statistics are aggregated and a summary is added to the data.
"""
def __init__(self, formatter):
self.formatter = formatter
def __enter__(self):
"""Write header upon entry."""
self.formatter.write_header()
return self
def append(self, basepairs, seqs, filename):
"""Append a new line for the given basepair num, sequences and file."""
self.formatter.append(
basepairs, seqs, basepairs / float(seqs), filename)
def __exit__(self, exc_type, exc_value, traceback):
"""No exception? Finalize the formatter on exit."""
if exc_type is None:
self.formatter.finalize()
class CsvFormatter(object):
"""Format the statistics information as CSV."""
headers = ['bp', 'seqs', 'avg_len', 'filename']
def __init__(self, underlying_file):
self.file = csv.writer(underlying_file)
def write_header(self):
"""Add headers for the csv columns."""
self.file.writerow(self.headers)
def append(self, basepairs, seqs, avg_len, filename):
"""Append the data separated by comma."""
self.file.writerow([basepairs, seqs, "%.1f" % avg_len, filename])
def finalize(self):
"""No statistics since the CSV data is to be processed further."""
pass
class StdFormatter(object):
"""Format the statistics in a human readable string."""
def __init__(self, underlying_file):
self.file = underlying_file
self.bp_total = 0
self.seqs_total = 0
def write_header(self):
"""Write a header line."""
self.file.write('---------------\n')
def append(self, basepairs, seqs, avg_len, filename):
"""Append the data human readable."""
self.bp_total += basepairs
self.seqs_total += seqs
self.file.write('%d bp / %d seqs; %.1f average length -- %s\n' %
(basepairs,
seqs,
avg_len,
filename))
def finalize(self):
"""Add a summary with the accumulated data."""
self.file.write('---------------\n')
avg = self.bp_total / float(self.seqs_total)
self.file.write('%d bp / %d seqs; %.1f average length -- total\n' %
(self.bp_total, self.seqs_total, avg))
def analyze_file(filename):
"""Run over the given file and count base pairs and sequences."""
bps = 0
seqs = 0
input_iter = screed.open(filename)
for record in input_iter:
if seqs % 100000 == 0:
print('...', filename, seqs, file=sys.stderr)
bps += len(record.sequence)
seqs += 1
return bps, seqs
def main():
"""Main function - run when executed as a script."""
args = sanitize_help(get_parser()).parse_args()
statistics = []
for filename in args.filenames:
try:
bps, seqs = analyze_file(filename)
except (IOError, OSError, EOFError) as exc:
print('ERROR in opening %s:' % filename, file=sys.stderr)
print(' ', str(exc), file=sys.stderr)
continue
if seqs:
statistics.append((bps, seqs, filename))
avg = bps / float(seqs)
msg = '%d bps / %d seqs; %.1f average length -- %s' % (bps,
seqs,
avg,
filename)
print('... found', msg, file=sys.stderr)
else:
print('No sequences found in %s' % filename, file=sys.stderr)
if statistics:
if args.csv:
formatter = CsvFormatter(args.outfp)
else:
formatter = StdFormatter(args.outfp)
with StatisticsOutput(formatter) as out:
for stat in statistics:
out.append(*stat)
else:
print('No sequences found in %d files' %
len(args.filenames), file=args.outfp)
if __name__ == '__main__':
main()
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