parallel_align_seqs_pynast.py
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/