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.. _parallel_assign_taxonomy_blast:
.. index:: parallel_assign_taxonomy_blast.py
*parallel_assign_taxonomy_blast.py* -- Parallel taxonomy assignment using BLAST
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
This script performs like the `assign_taxonomy.py <./assign_taxonomy.html>`_ script, but is intended to make use of multicore/multiprocessor environments to perform analyses in parallel.
**Usage:** :file:`parallel_assign_taxonomy_blast.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-i, `-`-input_fasta_fp
Full path to input_fasta_fp [REQUIRED]
-o, `-`-output_dir
Full path to store output files [REQUIRED]
**[OPTIONAL]**
-r, `-`-reference_seqs_fp
Ref seqs to blast against. Must provide either --blast_db or --reference_seqs_db for assignment with blast [default: /software/gg_97_otus_4feb2011.fasta]
-b, `-`-blast_db
Database to blast against. Must provide either --blast_db or --reference_seqs_db for assignment with blast [default: None]
-e, `-`-e_value
Maximum e-value to record an assignment, only used for blast method [default: 0.001]
-B, `-`-blastmat_dir
Full path to directory containing blastmat file [default: /software/blast-2.2.22/data]
-N, `-`-assign_taxonomy_fp
Full path to scripts/`assign_taxonomy.py <./assign_taxonomy.html>`_ [default: /Users/jistombaugh/Dropbox/Qiime_work/scripts/`assign_taxonomy.py <./assign_taxonomy.html>`_]
-O, `-`-jobs_to_start
Number of jobs to start [default: 1]
-P, `-`-poller_fp
Full path to qiime/parallel/`poller.py <./poller.html>`_ [default: /Users/jistombaugh/Dropbox/Qiime_work/scripts/`poller.py <./poller.html>`_]
-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/jistombaugh/Dropbox/Qiime_work/scripts/`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]
-Y, `-`-python_exe_fp
Full path to python executable [default: /Library/Frameworks/Python.framework/Versions/2.7/bin/python]
-Z, `-`-seconds_to_sleep
Number of seconds to sleep between checks for run completion when polling runs [default: 60]
-t, `-`-id_to_taxonomy_fp
Full path to id_to_taxonomy mapping file [default: /software/greengenes_tax_rdp_train.txt]
**Output:**
Mapping of sequence identifiers to taxonomy and quality scores.
**Example:**
Assign taxonomy to all sequences in the input file (-i) via five (-O) independent jobs using BLAST with the id to taxonomy mapping file (-t) and reference sequence template file (-r), and write the results (-o) to /home/qiime_user/out/. BE SURE TO SPECIFY FULL PATHS!
::
parallel_assign_taxonomy_blast.py -O 5 -i /home/qiime_user/inseqs.fasta -t /home/qiime_user/at_id_to_taxonomy.txt -r /home/qiime_user/at_refseqs.fasta -o /home/qiime_user/out/
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