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fasta_formatter - changes the width of sequences line in a FASTA file

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 0.0.14 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.
August 2017 fasta_formatter 0.0.14