parallel_assign_taxonomy_blast.py – Parallel taxonomy assignment using BLAST

Description:

This script performs like the assign_taxonomy.py script, but is intended to make use of multicore/multiprocessor environments to perform analyses in parallel.

Usage: 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 [default: /Users/jistombaugh/Dropbox/Qiime_work/scripts/assign_taxonomy.py]

-O, --jobs_to_start

Number of jobs to start [default: 1]

-P, --poller_fp

Full path to qiime/parallel/poller.py [default: /Users/jistombaugh/Dropbox/Qiime_work/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/jistombaugh/Dropbox/Qiime_work/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: /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/