fasta_formatter (1)

usage: fasta_formatter [-h] [-i INFILE] [-o OUTFILE] [-w N] [-t] [-e] Part of FASTX Toolkit 0.0.14 by [email protected]

[-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

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.