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.. _parallel_blast:
.. index:: parallel_blast.py
*parallel_blast.py* -- Parallel BLAST
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
This script for performing blast while making use of multicore/multiprocessor environments to perform analyses in parallel.
**Usage:** :file:`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 <./start_parallel_jobs.html>`_]
-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
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