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fasta_formatter - Online in the Cloud

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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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