parallel_align_seqs_pynast.py – Parallel sequence alignment using PyNAST

Description:

A wrapper for the align_seqs.py PyNAST option, intended to make use of multicore/multiprocessor environments to perform analyses in parallel.

Usage: parallel_align_seqs_pynast.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_fasta_fp

Path to the input fasta file

-o, --output_dir

Path to the output directory

[OPTIONAL]

-a, --pairwise_alignment_method

Method to use for pairwise alignments [default: uclust]

-d, --blast_db

Database to blast against [default: created on-the-fly from template_alignment]

-e, --min_length

Minimum sequence length to include in alignment [default: 75% of the median input sequence length]

-p, --min_percent_id

Minimum percent sequence identity to closest blast hit to include sequence in alignment [default: 75.0]

-O, --jobs_to_start

Number of jobs to start [default: 4]

-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]

-t, --template_fp

Filepath for template against [default: /Users/caporaso/data/greengenes_core_sets/core_set_aligned_imputed.fasta_11_8_07.no_dots]

Output:

This results in a multiple sequence alignment (FASTA-formatted).

Example:

Align the input file (-i) against using PyNAST and write the output (-o) to $PWD/pynast_aligned_seqs/. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/).

parallel_align_seqs_pynast.py -i $PWD/inseqs.fasta -o $PWD/pynast_aligned_seqs/