PyNAST(1) alignment of short DNA sequences


pynast [options] {-i input_fp -t template_fp}


[] indicates optional input (order unimportant) {} indicates required input (order unimportant)

Example usage:

pynast -i my_input.fasta -t my_template.fasta


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]
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