FASTA_FORMATTER(1) User Commands FASTA_FORMATTER(1)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 0.0.13.2 by gordon@cshl.edu
[-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
SEE ALSO
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.
fasta_formatter 0.0.13.2 May 2012 FASTA_FORMATTER(1)
Check Out this Related Man Page
HHCONSENSUS(1) User Commands HHCONSENSUS(1)NAME
hhconsensus - calculate the consensus sequence for an A3M/FASTA input file
SYNOPSIS
hhconsensus -i <file> [options]
DESCRIPTION
HHconsensus version 2.0.15 (June 2012) Calculate the consensus sequence for an A3M/FASTA input file. (C) Johannes Soeding, Michael Rem-
mert, Andreas Biegert, Andreas Hauser Remmert M, Biegert A, Hauser A, and Soding J. HHblits: Lightning-fast iterative protein sequence
searching by HMM-HMM alignment. Nat. Methods 9:173-175 (2011).
-i <file>
query alignment (A2M, A3M, or FASTA), or query HMM
Output options:
-s <file>
append consensus sequence in FASTA (default=<infile.seq>)
-o <file>
write alignment with consensus sequence in A3M
-oa3m <file>
same
-oa2m <file>
write alignment with consensus sequence in A2M
-ofas <file>
write alignment with consensus sequence in FASTA
-v <int>
verbose mode: 0:no screen output 1:only warings 2: verbose
Filter input alignment (options can be combined):
-id [0,100] maximum pairwise sequence identity (%) (def=100)
-diff [0,inf[ filter most diverse set of sequences, keeping at least this
many sequences in each block of >50 columns (def=0)
-cov [0,100] minimum coverage with query (%) (def=0)
-qid [0,100] minimum sequence identity with query (%) (def=0)
-qsc [0,100] minimum score per column with query (def=-20.0)
Input alignment format:
-M a2m use A2M/A3M (default): upper case = Match; lower case = Insert; '-' = Delete; '.' = gaps aligned to inserts (may be omitted)
-M first
use FASTA: columns with residue in 1st sequence are match states
-M [0,100]
use FASTA: columns with fewer than X% gaps are match states
Other options:
-addss add predicted secondary structure information from PSIPRED
Example: hhconsensus -i stdin -s stdout
hhconsensus 2.0.15 June 2012 HHCONSENSUS(1)