---
name: "fasta_formatter"
section: "1"
platform: "linux"
package: "fastx-toolkit"
version: "0.0.14-6"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/fasta_formatter"
---

# fasta\_formatter(1)

changes the width of sequences line in a FASTA file

## NAME

fasta\_formatter - changes the width of sequences line in a FASTA file

## DESCRIPTION

usage: fasta\_formatter \[-h\] \[-i INFILE\] \[-o OUTFILE\] \[-w N\] \[-t\] \[-e\] Part of FASTX Toolkit 0.0.14 by assafgordon@gmail.com

- \[-h\]

  \= This helpful help screen.

- \[-i INFILE\]

  \= FASTA/Q input file. default is STDIN.

-

  \[-o OUTFILE\] = FASTA/Q output file. default is STDOUT. \[-w N\]       = max. sequence line width for output FASTA file.

-

  When ZERO (the default), sequence lines will NOT be wrapped - all nucleotides of each sequences will appear on a single line (good for scripting).

- \[-t\]

  \= Output tabulated format (instead of FASTA format).

-

  Sequence-Identifiers will be on first column, Nucleotides will appear on second column (as single line).

- \[-e\]

  \= Output empty sequences (default is to discard them).

-

  Empty sequences are ones who have only a sequence identifier, but not actual nucleotides.

### Input Example:

-

  \>MY-ID AAAAAGGGGG CCCCCTTTTT AGCTN

### Output example with unlimited line width \[-w 0\]:

-

  \>MY-ID AAAAAGGGGGCCCCCTTTTTAGCTN

### Output example with max. line width=7 \[-w 7\]:

-

  \>MY-ID AAAAAGG GGGTTTT TCCCCCA GCTN

### Output example with tabular output \[-t\]:

- MY-ID

  AAAAAGGGGGCCCCCTTTTAGCTN

example of empty sequence: (will be discarded unless \[-e\] is used)

-

  \>REGULAR-SEQUENCE-1 AAAGGGTTTCCC \>EMPTY-SEQUENCE \>REGULAR-SEQUENCE-2 AAGTAGTAGTAGTAGT GTATTTTATAT

## SEE ALSO

The quality of this automatically generated manpage might be insufficient.  It is suggested to visit

-

  http://hannonlab.cshl.edu/fastx\_toolkit/commandline.html

to get a better layout as well as an overview about connected FASTX tools.