NAME¶
PyNAST - alignment of short DNA sequences
SYNOPSIS¶
pynast [
options]
{-i input_fp -t template_fp}
DESCRIPTION¶
[] indicates optional input (order unimportant) {} indicates required input
(order unimportant)
Example usage:¶
- pynast -i my_input.fasta -t
my_template.fasta
OPTIONS¶
- --version
- show program's version number and exit
- -h, --help
- show this help message and exit
- -t TEMPLATE_FP,
--template_fp=TEMPLATE_FP
- path to template alignment file [REQUIRED]
- -i INPUT_FP, --input_fp=INPUT_FP
- path to input fasta file [REQUIRED]
- -v, --verbose
- Print status and other information during execution
[default: False]
- -p MIN_PCT_ID,
--min_pct_id=MIN_PCT_ID
- minimum percent sequence identity to consider a sequence a
match [default: 75.0]
- -l MIN_LEN, --min_len=MIN_LEN
- minimum sequence length to include in NAST alignment
[default: 1000]
- -m PAIRWISE_ALIGNMENT_METHOD,
--pairwise_alignment_method= PAIRWISE_ALIGNMENT_METHOD
- method for performing pairwise alignment [default:
uclust]
- -a FASTA_OUT_FP,
--fasta_out_fp=FASTA_OUT_FP
- path to store resulting alignment file [default: derived
from input filepath]
- -g LOG_FP, --log_fp=LOG_FP
- path to store log file [default: derived from input
filepath]
- -f FAILURE_FP,
--failure_fp=FAILURE_FP
- path to store file of seqs which fail to align [default:
derived from input filepath]
- -e MAX_E_VALUE,
--max_e_value=MAX_E_VALUE
- Depreciated. Will be removed in PyNAST 1.2
- -d BLAST_DB, --blast_db=BLAST_DB
- Depreciated. Will be removed in PyNAST 1.2
SEE ALSO¶
http://pynast.sourceforge.net