FASTA_FORMATTER(1) User Commands FASTA_FORMATTER(1)
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 0.0.13.2 by gordon@cshl.edu
[-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.
fasta_formatter 0.0.13.2 May 2012 FASTA_FORMATTER(1)
