NAME¶

PyNAST - alignment of short DNA sequences

SYNOPSIS¶

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

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

--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