parallel_blast.py – Parallel BLAST

Description:

This script for performing blast while making use of multicore/multiprocessor environments to perform analyses in parallel.

Usage: parallel_blast.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --infile_path

Path of sequences to use as queries [REQUIRED]

-o, --output_dir

Name of output directory for blast jobs [REQUIRED]

[OPTIONAL]

-c, --disable_low_complexity_filter

Disable filtering of low-complexity sequences (i.e., -F F is passed to blast) [default: False]

-e, --e_value

E-value threshold for blasts [default: 1e-30]

-n, --num_hits

Number of hits per query for blast results [default: 1]

-w, --word_size

Word size for blast searches [default: 30]

-a, --blastmat_dir

Full path to directory containing blastmat file [default: /Applications/blast-2.2.22/data/]

-r, --refseqs_path

Path to fasta sequences to search against. Required if -b is not provided.

-b, --blast_db

Name of pre-formatted BLAST database. Required if -r is not provided.

-O, --jobs_to_start

Number of jobs to start [default: 2]

-R, --retain_temp_files

Retain temporary files after runs complete (useful for debugging) [default: False]

-S, --suppress_submit_jobs

Only split input and write commands file - don’t submit jobs [default: False]

-T, --poll_directly

Poll directly for job completion rather than running poller as a separate job. If -T is specified this script will not return until all jobs have completed. [default: False]

-U, --cluster_jobs_fp

Path to cluster jobs script (defined in qiime_config) [default: start_parallel_jobs.py]

-W, --suppress_polling

Suppress polling of jobs and merging of results upon completion [default: False]

-X, --job_prefix

Job prefix [default: descriptive prefix + random chars]

-Z, --seconds_to_sleep

Number of seconds to sleep between checks for run completion when polling runs [default: 1]

Output:

Example:

BLAST $PWD/inseqs.fasta (-i) against a blast database created from $PWD/refseqs.fasta (-r). Store the results in $PWD/blast_out/ (-o). ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/).

parallel_blast.py -i $PWD/inseqs.fasta -r $PWD/refseqs.fasta -o $PWD/blast_out/ -e 0.001