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parallel_map_reads_to_reference.py
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parallel_map_reads_to_reference.py
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#!/usr/bin/env python
# File created on 07 Jul 2012
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.7.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Release"
from qiime.util import (parse_command_line_parameters,
get_options_lookup,
make_option)
from qiime.parallel.map_reads_to_reference import \
(ParallelDatabaseMapperUsearch, ParallelDatabaseMapperBlat, ParallelDatabaseMapperBwaShort)
options_lookup = get_options_lookup()
script_info = {}
script_info['brief_description'] = ""
script_info['script_description'] = ""
script_info['script_usage'] = [("","","%prog -i $PWD/query_nt.fasta -r $PWD/refseqs_pr.fasta -o $PWD/usearch_mapped"),
("","","%prog -i $PWD/query_nt.fasta -r $PWD/refseqs_pr.fasta -o $PWD/blat_mapped -m blat"),
("","","%prog -i $PWD/query_nt.fasta -r $PWD/refseqs_nt.fasta -o $PWD/bwa-short_mapped -m bwa-short")]
script_info['output_description']= ""
script_info['required_options'] = [
make_option('-i', '--input_seqs_filepath',type='existing_filepath',
help='Path to input sequences file'),
make_option('-o', '--output_dir',type='new_dirpath',
help='Directory to store results'),
make_option('-r', '--refseqs_fp',type='existing_filepath',
help='Path to reference sequences'),
]
script_info['optional_options'] = [
make_option('-t', '--observation_metadata_fp',type='existing_filepath',
help=('Path to observation metadata (e.g., taxonomy, EC, etc) [default: %default]')),
make_option('-m', '--assignment_method', type='choice',
choices=['usearch','blat','bwa-short'], default = "usearch",
help=('Method for picking OTUs. Valid choices are: ' +\
' '.join(['usearch','blat','bwa-short']) +\
'. [default: %default]')),
make_option('-e', '--evalue', type='float', default=1e-10,
help=('Max e-value to consider a match [default: %default]')),
make_option('-s', '--min_percent_id', type='float', default=0.75,
help=('Min percent id to consider a match [default: %default]')),
make_option('--max_diff', type='float', default=None,
help=('maxDiff to consider a match (applicable for -m bwa) -- '
'see the aln section of "man bwa" for details '
'[default (defined by bwa): 0.04]')),
make_option('--queryalnfract', type='float', default=0.35,
help=('Min percent of the query seq that must match to consider a match (usearch only) [default: %default]')),
make_option('--targetalnfract', type='float', default=0.0,
help=('Min percent of the target/reference seq that must match to consider a match (usearch only) [default: %default]')),
make_option('--max_accepts',type='int',default=1,
help="max_accepts value (usearch only) [default: %default]"),
make_option('--max_rejects',type='int',default=32,
help="max_rejects value to (usearch only) [default: %default]"),
options_lookup['jobs_to_start'],
options_lookup['retain_temp_files'],
options_lookup['suppress_submit_jobs'],
options_lookup['poll_directly'],
options_lookup['cluster_jobs_fp'],
options_lookup['suppress_polling'],
options_lookup['job_prefix'],
options_lookup['seconds_to_sleep']
]
script_info['version'] = __version__
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
params = eval(str(opts))
params['save_uc_files'] = True
if opts.assignment_method == 'usearch':
parallel_runner = ParallelDatabaseMapperUsearch(
cluster_jobs_fp=opts.cluster_jobs_fp,
jobs_to_start=opts.jobs_to_start,
retain_temp_files=opts.retain_temp_files,
suppress_polling=opts.suppress_polling,
seconds_to_sleep=opts.seconds_to_sleep)
parallel_runner(opts.input_seqs_filepath,
opts.output_dir,
params,
job_prefix=opts.job_prefix,
poll_directly=opts.poll_directly,
suppress_submit_jobs=False)
elif opts.assignment_method == 'blat':
parallel_runner = ParallelDatabaseMapperBlat(
cluster_jobs_fp=opts.cluster_jobs_fp,
jobs_to_start=opts.jobs_to_start,
retain_temp_files=opts.retain_temp_files,
suppress_polling=opts.suppress_polling,
seconds_to_sleep=opts.seconds_to_sleep)
parallel_runner(opts.input_seqs_filepath,
opts.output_dir,
params,
job_prefix=opts.job_prefix,
poll_directly=opts.poll_directly,
suppress_submit_jobs=False)
elif opts.assignment_method == 'bwa-short':
# cast max_diff to an int if it's being passed as an int
if params['max_diff'] != None and params['max_diff'] > 1.0:
params['max_diff'] = int(params['max_diff'])
parallel_runner = ParallelDatabaseMapperBwaShort(
cluster_jobs_fp=opts.cluster_jobs_fp,
jobs_to_start=opts.jobs_to_start,
retain_temp_files=opts.retain_temp_files,
suppress_polling=opts.suppress_polling,
seconds_to_sleep=opts.seconds_to_sleep)
parallel_runner(opts.input_seqs_filepath,
opts.output_dir,
params,
job_prefix=opts.job_prefix,
poll_directly=opts.poll_directly,
suppress_submit_jobs=False)
else:
## other -- shouldn't be able to get here as a KeyError would have
## been raised earlier
raise ValueError, "Unknown read mapping method: %s" % opts.assignment_method
if __name__ == "__main__":
main()