parallel_identify_chimeric_seqs.py – Parallel chimera detection

Description:

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

Usage: parallel_identify_chimeric_seqs.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_fasta_fp

Path to the input fasta file

[OPTIONAL]

-a, --aligned_reference_seqs_fp

Path to (Py)Nast aligned reference sequences. REQUIRED when method ChimeraSlayer [default: None]

-t, --id_to_taxonomy_fp

Path to tab-delimited file mapping sequences to assigned taxonomy. Each assigned taxonomy is provided as a comma-separated list. [default: None; REQUIRED when method is blast_fragments]

-r, --reference_seqs_fp

Path to reference sequences (used to build a blast db when method blast_fragments). [default: None; REQUIRED when method blast_fragments if no blast_db is provided;]

-b, --blast_db

Database to blast against. Must provide either –blast_db or –reference_seqs_fp when method is blast_fragments [default: None]

-m, --chimera_detection_method

Chimera detection method. Choices: blast_fragments or ChimeraSlayer. [default:ChimeraSlayer]

-n, --num_fragments

Number of fragments to split sequences into (i.e., number of expected breakpoints + 1) [default: 3]

-d, --taxonomy_depth

Number of taxonomic divisions to consider when comparing taxonomy assignments [default: 4]

-e, --max_e_value

Max e-value to assign taxonomy [default: 1e-30]

--min_div_ratio

Min divergence ratio (passed to ChimeraSlayer). If set to None uses ChimeraSlayer default value. [default: None]

-o, --output_fp

Path to store output [default: derived from input_seqs_fp]

-N, --identify_chimeric_seqs_fp

Full path to scripts/identify_chimeric_seqs.py [default: /Users/jistombaugh/Dropbox/Qiime_work/scripts/identify_chimeric_seqs.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]

Output:

The result of parallel_identify_chimeric_seqs.py is a text file that identifies which sequences are chimeric.

blast_fragments example:

For each sequence provided as input, the blast_fragments method splits the input sequence into n roughly-equal-sized, non-overlapping fragments, and assigns taxonomy to each fragment against a reference database. The BlastTaxonAssigner (implemented in assign_taxonomy.py) is used for this. The taxonomies of the fragments are compared with one another (at a default depth of 4), and if contradictory assignments are returned the sequence is identified as chimeric. For example, if an input sequence was split into 3 fragments, and the following taxon assignments were returned:

fragment1:	Archaea;Euryarchaeota;Methanobacteriales;Methanobacterium
fragment2:	Archaea;Euryarchaeota;Halobacteriales;uncultured
fragment3:	Archaea;Euryarchaeota;Methanobacteriales;Methanobacterium

The sequence would be considered chimeric at a depth of 3 (Methanobacteriales vs. Halobacteriales), but non-chimeric at a depth of 2 (all Euryarchaeota).

blast_fragments begins with the assumption that a sequence is non-chimeric, and looks for evidence to the contrary. This is important when, for example, no taxonomy assignment can be made because no blast result is returned. If a sequence is split into three fragments, and only one returns a blast hit, that sequence would be considered non-chimeric. This is because there is no evidence (i.e., contradictory blast assignments) for the sequence being chimeric. This script can be run by the following command, where the resulting data is written to the directory “identify_chimeras/” and using default parameters (e.g. chimera detection method (“-m blast_fragments”), number of fragments (“-n 3”), taxonomy depth (“-d 4”) and maximum E-value (“-e 1e-30”)):

parallel_identify_chimeric_seqs.py -i repr_set_seqs.fasta -t taxonomy_assignment.txt -r ref_seq_set.fna -o chimeric_seqs.txt

ChimeraSlayer Example:

Identify chimeric sequences using the ChimeraSlayer algorithm against a user provided reference database. The input sequences need to be provided in aligned (Py)Nast format and the reference database needs to be provided as aligned FASTA (-a). Note that the reference database needs to be the same that was used to build the alignment of the input sequences!

parallel_identify_chimeric_seqs.py -m ChimeraSlayer -i repr_set_seqs_aligned.fasta -a ref_seq_set_aligned.fasta -o chimeric_seqs.txt