pullseq(1)

pullseq1

<short_description>

Overview

pullseq - a bioinformatics tool for manipulating fasta and fastq files

Version: 1.0.2 Name lookup method: UTHASH (Written by bct - copyright 2012-2015)

Usage:

: pullseq -i <input fasta/fastq file> -n <header names to select>

: pullseq -i <input fasta/fastq file> -m <minimum sequence length>

: pullseq -i <input fasta/fastq file> -g <regex name to match>

: pullseq -i <input fasta/fastq file> -m <minimum sequence length> -a <max sequence length>

: pullseq -i <input fasta/fastq file> -t

: cat <names to select from STDIN> | pullseq -i <input fasta/fastq file> -N

: Options:

-i, --input,: Input fasta/fastq file (required)

-n, --names,: File of header id names to search for

-N, --names_stdin, Use STDIN for header id names

`-g, --regex,`	Regular expression to match (PERL compatible; always case-insensitive)
`-m, --min,`	Minimum sequence length
`-a, --max,`	Maximum sequence length
`-l, --length,`	Sequence characters per line (default 50)
`-c, --convert,`	Convert input to fastq/fasta (e.g. if input is fastq, output will be fasta)
`-q, --quality,`	ASCII code to use for fasta->fastq quality conversions
`-e, --excluded,`	Exclude the header id names in the list (`-n`)
`-t, --count,`	Just count the possible output, but don't write it
`-h, --help,`	Display this help and exit
`-v, --verbose,`	Print extra details during the run
`--version,`	Output version information and exit

Releases

Unchanged in 2 releases since Debian 12 (Bookworm).

12–13