Command line reference for PASR

Table of contents

• pasr
• build
• search
• get_hit_seqs
• max_score
• bsr
• pasr_plot
• pasr_select

pasr

usage: aastk pasr [-h] -q QUERY -s SEED [-o OUTPUT] [-m MATRIX] [-n THREADS] [-d DB_PATH] [-k KEY_COLUMN] [-b BLOCK] [-c CHUNK] [--sensitivity {fast,sensitive,mid-sensitive,very-sensitive,ultra-sensitive,faster}] [--update] [-y YAML] [--sql] [--keep] [--svg] [--force]

Options:

-h, --help
        Show this help message and exit

Required arguments:

-q, --query QUERY
        Path to query FASTA
-s, --seed SEED
        Path to FASTA files containing seed sequences for database creation

Optional:

-o, --output OUTPUT
        Desired output directory (default: current working directory)
-m, --matrix MATRIX
        Choose BLOSUM substitution matrix (BLOSUM 45 or BLOSUM 62)
-n, --threads THREADS
        Number of threads to be used (default: 1)
-d, --db_path DB_PATH
        Path to SQLite database
-k, --key_column KEY_COLUMN
        Column index in the BLAST tab file to pull unique IDs from (default is 0)
-b, --block BLOCK
        Choose diamond blastp sequence block size in billions of letters (default: 6)
-c, --chunk CHUNK
        Choose number of chunks for diamond blastp index processing (default: 2)
--sensitivity {fast,sensitive,mid-sensitive,very-sensitive,ultra-sensitive,faster}
        Set the sensitivity level for the DIAMOND search: fast, sensitive, mid-sensitive, very-sensitive, ultra-sensitive, or faster (default: fast)
--update
        Update subset of data using metadata yaml file
-y, --yaml YAML
        Path to metadata yaml file
--sql
        Use AASTK SQLite database for sequence retrieval
--keep
        Keep intermediate files in specified paths
--svg
        Generate plot in SVG format
--force
        Set flag to overwrite existing files in specified path

 

build

usage: aastk build [-h] -s SEED -d DB [-n THREADS] [--force]

Options:

-h, --help
        Show this help message and exit

Required arguments:

-s, --seed SEED
        Path to FASTA files containing seed sequences for database creation
-d, --db DB
        Specify path to DIAMOND database

Optional:

-n, --threads THREADS
        Number of threads to be used (default: 1)
--force
        Set flag to overwrite existing files in specified path

 

search

usage: aastk search [-h] -d DB -q QUERY [-o OUTPUT] [-n THREADS] [-b BLOCK] [-c CHUNK] [--sensitivity {fast,sensitive,mid-sensitive,very-sensitive,ultra-sensitive,faster}] [--force]

Options:

-h, --help
        Show this help message and exit

Required arguments:

-d, --db DB
        Specify path to DIAMOND database
-q, --query QUERY
        Path to query FASTA

Optional:

-o, --output OUTPUT
        Desired output directory (default: current working directory)
-n, --threads THREADS
        Number of threads to be used (default: 1)
-b, --block BLOCK
        Choose diamond blastp sequence block size in billions of letters (default: 6)
-c, --chunk CHUNK
        Choose number of chunks for diamond blastp index processing (default: 2)
--sensitivity {fast,sensitive,mid-sensitive,very-sensitive,ultra-sensitive,faster}
        Set the sensitivity level for the DIAMOND search: fast, sensitive, mid-sensitive, very-sensitive, ultra-sensitive, or faster (default: fast)
--force
        Set flag to overwrite existing files in specified path

 

get_hit_seqs

usage: aastk get_hit_seqs [-h] (--sql | -q QUERY) -t TABULAR [-o OUTPUT] [-d DB_PATH] [-n THREADS] [-k KEY_COLUMN] [--force]

Options:

-h, --help
        Show this help message and exit

Mutually exclusive required arguments:

--sql
        Use AASTK SQLite database for sequence retrieval
-q, --query QUERY
        Path to query FASTA

Required arguments:

-t, --tabular TABULAR
        Path to tabular BLAST/DIAMOND output file

Optional:

-o, --output OUTPUT
        Desired output directory (default: current working directory)
-d, --db_path DB_PATH
        Path to SQLite database
-n, --threads THREADS
        Number of threads to be used (default: 1)
-k, --key_column KEY_COLUMN
        Column index in the BLAST tab file to pull unique IDs from (default is 0)
--force
        Set flag to overwrite existing files in specified path

 

max_score

usage: aastk max_score [-h] -e EXTRACTED [-o OUTPUT] [-m MATRIX] [--force]

Options:

-h, --help
        Show this help message and exit

Required arguments:

-e, --extracted EXTRACTED
        Path to FASTA file containing extracted matching sequences

Optional:

-o, --output OUTPUT
        Desired output directory (default: current working directory)
-m, --matrix MATRIX
        Choose BLOSUM substitution matrix (BLOSUM 45 or BLOSUM 62)
--force
        Set flag to overwrite existing files in specified path

 

bsr

usage: aastk bsr [-h] (-c COLUMN_INFO_PATH | -s SCORE_COLUMN) -t TABULAR -m MAX_SCORES [-o OUTPUT] [-k KEY_COLUMN] [--force]

Options:

-h, --help
        Show this help message and exit

Mutually exclusive required arguments:

-c, --column_info_path COLUMN_INFO_PATH
        Path to json file containing columns the blast output file generated by aastk search
-s, --score_column SCORE_COLUMN
        Index of the raw score column of BLAST tabular output file. Counting starts at 1

Required arguments:

-t, --tabular TABULAR
        Path to tabular BLAST/DIAMOND output file
-m, --max_scores MAX_SCORES
        Path to file containing max self scores

Optional:

-o, --output OUTPUT
        Desired output directory (default: current working directory)
-k, --key_column KEY_COLUMN
        Column index in the BLAST tab file to pull unique IDs from (default is 0)
--force
        Set flag to overwrite existing files in specified path

 

pasr_plot

usage: aastk pasr_plot [-h] -b BSR [-o OUTPUT] [--svg] [--force] [--update] [-y YAML]

Options:

-h, --help
        Show this help message and exit

Required arguments:

-b, --bsr BSR
        Path to blast score ratio input file

Optional:

-o, --output OUTPUT
        Desired output directory (default: current working directory)
--svg
        Generate plot in SVG format
--force
        Set flag to overwrite existing files in specified path
--update
        Update subset of data using metadata yaml file
-y, --yaml YAML
        Path to metadata yaml file

 

pasr_select

usage: aastk pasr_select [-h] (-y YAML | --params) -m MATCHED --bsr BSR [-o OUTPUT] [--create_yaml] [-l SELFMIN] [-u SELFMAX] [-d DBMIN] [-b BSR_CUTOFF] [--force]

Options:

-h, --help
        Show this help message and exit

Mutually exclusive required arguments:

-y, --yaml YAML
        Path to metadata yaml file
--params
        Select subset of matched sequences based on command line parameters

Required arguments:

-m, --matched MATCHED
        FASTA file containing matched sequences from previous PASR run
--bsr BSR
        Path to blast score ratio input file

Optional:

-o, --output OUTPUT
        Desired output directory (default: current working directory)
--create_yaml
        Create metadata yaml file from command line parameters
-l, --selfmin SELFMIN
        Lower cutoff for self score range to be included in updated dataset
-u, --selfmax SELFMAX
        Upper cutoff for self score range to be included in updated dataset
-d, --dbmin DBMIN
        Lower database score cutoff for inclusion in updated dataset
-b, --bsr_cutoff BSR_CUTOFF
        Blast Score Ratio cutoff for inclusion in updated dataset
--force
        Set flag to overwrite existing files in specified path