sampling-utils - Resampling Utilities

Overview

New in version 0.3.1.

Resampling Utilities

sample command

This command samples from a Fasta or FastQ file, based on a probability defined by the user (0.001 or 1 / 1000 by default, -r parameter), for a maximum number of sequences (100,000 by default, -x parameter). By default 1 sample is extracted, but as many as desired can be taken, by using the -n parameter.

The sequence file in input can be either be passed to the standard input or as last parameter on the command line. By defult a Fasta is expected, unless the -q parameter is passed.

The -p parameter specifies the prefix to be used, and if the output files can be gzipped using the -z parameter.

Options

Sampling utilities

usage: sampling-utils [-h] [-v | --quiet] [--cite] [--manual] [--version]
                      {sample} ...

Named Arguments

-v, --verbose	more verbose - includes debug messages Default: 20
--quiet	less verbose - only error and critical messages
--cite	Show citation for the framework
--manual	Show the script manual
--version	show program’s version number and exit

Sub-commands:

sample

Sample a Fasta/FastQ

sampling-utils sample [-h] [-p PREFIX] [-n NUMBER] [-r PROB] [-x MAX_SEQ] [-q]
                      [-z] [-v | --quiet] [--cite] [--manual] [--version]
                      [input_file]

Positional Arguments

input_file

Input FASTA file, defaults to stdin Default: -

Named Arguments

-p, --prefix	Prefix for the file name(s) in output Default: “sample”
-n, --number	Number of samples to take Default: 1
-r, --prob	Probability of picking a sequence Default: 0.001
-x, --max-seq	Maximum number of sequences Default: 100000
-q, --fastq	The input file is a fastq file Default: False
-z, --gzip	gzip output files Default: False
-v, --verbose	more verbose - includes debug messages Default: 20
--quiet	less verbose - only error and critical messages
--cite	Show citation for the framework
--manual	Show the script manual
--version	show program’s version number and exit