.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.
.TH FASTA_FORMATTER "1" "September 2018" "fasta_formatter 0.0.14" "User Commands"
.SH NAME
fasta_formatter \- changes the width of sequences line in a FASTA file
.SH DESCRIPTION
usage: fasta_formatter [\-h] [\-i INFILE] [\-o OUTFILE] [\-w N] [\-t] [\-e]
Part of FASTX Toolkit 0.0.14 by assafgordon@gmail.com
.TP
[\-h]
= This helpful help screen.
.TP
[\-i INFILE]
= FASTA/Q input file. default is STDIN.
.IP
[\-o OUTFILE] = FASTA/Q output file. default is STDOUT.
[\-w N]       = max. sequence line width for output FASTA file.
.IP
When ZERO (the default), sequence lines will NOT be wrapped \-
all nucleotides of each sequences will appear on a single
line (good for scripting).
.TP
[\-t]
= Output tabulated format (instead of FASTA format).
.IP
Sequence\-Identifiers will be on first column,
Nucleotides will appear on second column (as single line).
.TP
[\-e]
= Output empty sequences (default is to discard them).
.IP
Empty sequences are ones who have only a sequence identifier,
but not actual nucleotides.
.SS "Input Example:"
.IP
>MY\-ID
AAAAAGGGGG
CCCCCTTTTT
AGCTN
.SS "Output example with unlimited line width [-w 0]:"
.IP
>MY\-ID
AAAAAGGGGGCCCCCTTTTTAGCTN
.SS "Output example with max. line width=7 [-w 7]:"
.IP
>MY\-ID
AAAAAGG
GGGTTTT
TCCCCCA
GCTN
.SS "Output example with tabular output [-t]:"
.TP
MY\-ID
AAAAAGGGGGCCCCCTTTTAGCTN
.PP
example of empty sequence:
(will be discarded unless [\-e] is used)
.IP
>REGULAR\-SEQUENCE\-1
AAAGGGTTTCCC
>EMPTY\-SEQUENCE
>REGULAR\-SEQUENCE\-2
AAGTAGTAGTAGTAGT
GTATTTTATAT
.SH SEE ALSO
The quality of this automatically generated manpage might be
insufficient.  It is suggested to visit
.IP
http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
.P
to get a better layout as well as an overview about connected
FASTX tools.