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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
.TH PULLSEQ "1" "March 2021" "pullseq 1.0.2" "User Commands"
.SH NAME
pullseq \- <short_description>
.SH DESCRIPTION
pullseq \- a bioinformatics tool for manipulating fasta and fastq files
.PP
Version: 1.0.2 Name lookup method: UTHASH
(Written by bct \- copyright 2012\-2015)
.SS "Usage:"
.IP
pullseq \fB\-i\fR <input fasta/fastq file> \fB\-n\fR <header names to select>
.IP
pullseq \fB\-i\fR <input fasta/fastq file> \fB\-m\fR <minimum sequence length>
.IP
pullseq \fB\-i\fR <input fasta/fastq file> \fB\-g\fR <regex name to match>
.IP
pullseq \fB\-i\fR <input fasta/fastq file> \fB\-m\fR <minimum sequence length> \fB\-a\fR <max sequence length>
.IP
pullseq \fB\-i\fR <input fasta/fastq file> \fB\-t\fR
.IP
cat <names to select from STDIN> | pullseq \fB\-i\fR <input fasta/fastq file> \fB\-N\fR
.IP
Options:
.TP
\fB\-i\fR, \fB\-\-input\fR,
Input fasta/fastq file (required)
.TP
\fB\-n\fR, \fB\-\-names\fR,
File of header id names to search for
.HP
\fB\-N\fR, \fB\-\-names_stdin\fR, Use STDIN for header id names
.TP
\fB\-g\fR, \fB\-\-regex\fR,
Regular expression to match (PERL compatible; always case\-insensitive)
.TP
\fB\-m\fR, \fB\-\-min\fR,
Minimum sequence length
.TP
\fB\-a\fR, \fB\-\-max\fR,
Maximum sequence length
.TP
\fB\-l\fR, \fB\-\-length\fR,
Sequence characters per line (default 50)
.TP
\fB\-c\fR, \fB\-\-convert\fR,
Convert input to fastq/fasta (e.g. if input is fastq, output will be fasta)
.TP
\fB\-q\fR, \fB\-\-quality\fR,
ASCII code to use for fasta\->fastq quality conversions
.TP
\fB\-e\fR, \fB\-\-excluded\fR,
Exclude the header id names in the list (\fB\-n\fR)
.TP
\fB\-t\fR, \fB\-\-count\fR,
Just count the possible output, but don't write it
.TP
\fB\-h\fR, \fB\-\-help\fR,
Display this help and exit
.TP
\fB\-v\fR, \fB\-\-verbose\fR,
Print extra details during the run
.TP
\fB\-\-version\fR,
Output version information and exit
.SH AUTHOR
This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.
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