---
name: "geneparse"
section: "1"
platform: "linux"
package: "murasaki"
version: "1.68.6-14+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/geneparse"
---

# geneparse(1)

sequence file loader frontend

## NAME

geneparse - sequence file loader frontend

## SYNAPSE

geneparse \[options...\] \[input\] \[input2 ...\] #read input and write to stdout

## DESCRIPTION

Reads a sequence file and writes it somewhere (by default to stdout).

A specific range within an input file can be specified by file\[start,stop\].  The square brackets can be interchanged for any of {\[()\]}, (eg.  "genome.fa\[3000,4000\]" or "genome.fa{3000~4000}").  Be aware that all of those might be parsed by your shell.  Also any non-word character can be used to separate the numbers.

## OPTIONS

- \--repeatmask\|-r

  use soft-repeatmasked sequences (ie: replace lowercase bases with N's).

- \--upper\|--unmask\|-U

  ```
   uppercase all bases.
  ```

- \--length\|-l

  just print the length and exit

- \--clean\|-c

  don't append a new line when finished

- \--version\|-V

  prints the program version

- \--help\|-h

  prints a help message

- \--output\|-o

  send output to a file (otherwise use stdout). --output implies --clean.

- \--quiet\|-q

  silence all warnings

- \--verbose\|-v

  prints lots of extra details

## LICENSE

GNU General Public License, version 3 (GPLv3)

## AVAILABILITY

\<http://murasaki.sourceforge.net\>

## AUTHOR

Kris Popendorf \<krisp@dna.bio.keio.ac.jp\>

## SEE ALSO

[*murasaki*(1)](/murasaki/1.md), [*geneparse*(1)](/geneparse/1.md)