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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]
-r, --refseqs_path
Path to fasta sequences to search against [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]
-D, --suppress_format_blastdb
Supress format of blastdb [default: False]
-a, --blastmat_dir
Full path to directory containing blastmat file [default: /Applications/blast-2.2.22/data/]
-b, --blastall_fp
Path to blastall [default: blastall]
-O, --jobs_to_start
Number of jobs to start [default: 2]
-P, --poller_fp
Full path to qiime/parallel/poller.py [default: /Users/caporaso/code/Qiime/scripts/poller.py]
-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: /Users/caporaso/code/Qiime/scripts/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]
-Y, --python_exe_fp
Full path to python executable [default: python]
-Z, --seconds_to_sleep
Number of seconds to sleep between checks for run completion when polling runs [default: 6]

Output:

Example:

BLAST /home/qiime_user/10_seq.fasta (-i) via three (-O) independent jobs against a blast database created from /home/qiime_user/1000_seq.fasta (-r). Store the results in /home/qiime_user/bla_out/ (-o).

parallel_blast.py -i /home/qiime_user/10_seq.fasta -r /home/qiime_user/1000_seq.fasta -O 3 -o /home/qiime_user/bla_out/

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