/usr/lib/khmer/bin/count-median.py is in khmer 2.0+dfsg-5.
This file is owned by root:root, with mode 0o755.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 | #!/usr/bin/python3
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2012-2015, Michigan State University.
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# Contact: khmer-project@idyll.org
# pylint: disable=missing-docstring,invalid-name
"""
Count the median/avg k-mer abundance for each sequence in the input file.
The abundance is based on the k-mer counts in the given k-mer countgraph.
Can be used to estimate expression levels (mRNAseq) or coverage
(genomic/metagenomic).
% scripts/count-median.py <htname> <input seqs> <output counts>
Use '-h' for parameter help.
The output file contains sequence id, median, average, stddev, and seq length.
NOTE: All 'N's in the input sequences are converted to 'A's.
"""
from __future__ import print_function
import screed
import argparse
import sys
import csv
import textwrap
from khmer import __version__, load_countgraph
from khmer.kfile import check_input_files, check_space
from khmer.khmer_args import (info, sanitize_help, ComboFormatter,
_VersionStdErrAction)
def get_parser():
epilog = """\
Count the median/avg k-mer abundance for each sequence in the input file,
based on the k-mer counts in the given k-mer countgraph. Can be used
to estimate expression levels (mRNAseq) or coverage (genomic/metagenomic).
The output file contains sequence id, median, average, stddev, and
seq length, in comma-separated value (CSV) format.
Example::
load-into-countgraph.py counts tests/test-data/test-reads.fq.gz
count-median.py counts tests/test-data/test-reads.fq.gz medians.txt
NOTE: All 'N's in the input sequences are converted to 'A's.
"""
parser = argparse.ArgumentParser(
description='Count k-mers summary stats for sequences',
epilog=textwrap.dedent(epilog), formatter_class=ComboFormatter)
parser.add_argument('countgraph', metavar='input_count_graph_filename',
help='input k-mer countgraph filename')
parser.add_argument('input', metavar='input_sequence_filename',
help='input FAST[AQ] sequence filename')
parser.add_argument('output', metavar='output_summary_filename',
help='output summary filename',
type=argparse.FileType('w'))
parser.add_argument('--version', action=_VersionStdErrAction,
version='khmer {v}'.format(v=__version__))
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exists')
return parser
def main():
info('count-median.py', ['diginorm'])
args = sanitize_help(get_parser()).parse_args()
htfile = args.countgraph
input_filename = args.input
output = args.output
infiles = [htfile, input_filename]
for infile in infiles:
check_input_files(infile, args.force)
check_space(infiles, args.force)
print('loading k-mer countgraph from', htfile, file=sys.stderr)
countgraph = load_countgraph(htfile)
ksize = countgraph.ksize()
print('writing to', output.name, file=sys.stderr)
output = csv.writer(output)
# write headers:
output.writerow(['name', 'median', 'average', 'stddev', 'seqlen'])
for record in screed.open(input_filename):
seq = record.sequence.upper()
if 'N' in seq:
seq = seq.replace('N', 'A')
if ksize <= len(seq):
medn, ave, stdev = countgraph.get_median_count(seq)
ave, stdev = [round(x, 9) for x in (ave, stdev)]
output.writerow([record.name, medn, ave, stdev, len(seq)])
if __name__ == '__main__':
main()
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