pynast1
Alignment of short dna sequences
Usage
pynast [options]
-i
input_fp
-t
template_fp
Overview
[] indicates optional input (order unimportant) {} indicates required input (order unimportant)
Example usage:
-
pynast
-imy_input.fasta-tmy_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
Releases
Unchanged in 4 releases since Debian 7 (Wheezy).