DESCRIPTIONusage: fasta_formatter [-h] [-i INFILE] [-o OUTFILE] [-w N] [-t] [-e] Part of FASTX Toolkit 0.0.14 by [email protected]
- = 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).
- = Output tabulated format (instead of FASTA format).
- Sequence-Identifiers will be on first column, Nucleotides will appear on second column (as single line).
- = 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
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]:
example of empty sequence: (will be discarded unless [-e] is used)
- >REGULAR-SEQUENCE-1 AAAGGGTTTCCC >EMPTY-SEQUENCE >REGULAR-SEQUENCE-2 AAGTAGTAGTAGTAGT GTATTTTATAT