fasta_formatter1
Changes the width of sequences line in a fasta file
Overview
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]:
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>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
History
- Debian 10 (Buster): the text shown here
- Debian 9 (Stretch)
- Debian 8 (Jessie)
- Debian 7 (Wheezy)