This is the command fasta_formatter that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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