fasta_formatter - changes the width of sequences line in a FASTA
file
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.
- >MY-ID AAAAAGGGGG CCCCCTTTTT AGCTN
- >MY-ID AAAAAGGGGGCCCCCTTTTTAGCTN
- >MY-ID AAAAAGG GGGTTTT TCCCCCA GCTN
- 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
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.