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#!/usr/bin/env python
# File created on 09 Feb 2010
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.8.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
from os.path import splitext, split, exists, abspath, join
from qiime.util import (make_option,
parse_command_line_parameters,
create_dir,
load_qiime_config,
get_qiime_temp_dir)
from qiime.map_reads_to_reference import (usearch_database_mapper,
blat_database_mapper,
blat_nt_database_mapper,
bwa_sw_database_mapper,
bwa_short_database_mapper)
qiime_config = load_qiime_config()
assignment_functions = {'usearch':usearch_database_mapper,
'blat':blat_database_mapper,
'blat-nt':blat_nt_database_mapper,
'bwa-short':bwa_short_database_mapper,
'bwa-sw':bwa_sw_database_mapper}
script_info={}
script_info['brief_description'] = """ Script for performing assignment of reads against a reference database """
script_info['script_description'] = """ """
script_info['script_usage'] = []
script_info['script_usage'].append(("""""","""Run assignment with usearch using default parameters""","""%prog -i query_nt.fasta -r refseqs_pr.fasta"""))
script_info['script_usage'].append(("""""","""Run nucleotide versus protein BLAT using default parameters""","""%prog -i query_nt.fasta -r refseqs_pr.fasta -m blat"""))
script_info['script_usage'].append(("""""","""Run nucleotide versus protein BLAT using scricter e-value threshold""","""%prog -i query_nt.fasta -r refseqs_pr.fasta -o blat_mapped_strict/ -e 1e-70 -m blat"""))
script_info['script_usage'].append(("""""","""Run nucleotide versus nucleotide BLAT with default parameters""","""%prog -i query_nt.fasta -r refseqs_nt.fasta -m blat-nt"""))
script_info['script_usage'].append(("""""","""Run assignment with bwa-short using default parameters. bwa-short is intended to be used for reads up to 200bp. WARNING: reference sequences must be dereplicated! No matches will be found to reference sequences which show up multiple times (even if their sequence identifiers are different)!""","""%prog -i query_nt.fasta -r refseqs_nt.fasta -m bwa-short"""))
script_info['script_usage'].append(("""""","""Run assignment with bwa-sw using default parameters. WARNING: reference sequences must be dereplicated! No matches will be found to reference sequences which show up multiple times (even if their sequence identifiers are different)!""","""%prog -i query_nt.fasta -r refseqs_nt.fasta -m bwa-sw"""))
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('-r', '--refseqs_fp',type='existing_filepath',
help=('Path to reference sequences to search against [default: %default]')),
]
script_info['optional_options'] = [
make_option('-m', '--assignment_method', type='choice',
choices=assignment_functions.keys(), default = "usearch",
help=('Method for picking OTUs. Valid choices are: ' +\
', '.join(assignment_functions.keys()) +\
'. [default: %default]')),
make_option('-t', '--observation_metadata_fp',type='existing_filepath',
help=('Path to observation metadata (e.g., taxonomy, EC, etc) [default: %default]')),
make_option('-o', '--output_dir',type='new_dirpath',\
help=('Path to store result file '
'[default: ./<METHOD>_mapped/]')),
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('--genetic_code', type='int', default=11,
help=('ID of genetic code to use for DNA translations (please see '
'http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi) '
'Only valid with -m blat. [default: %default]')),
make_option('--max_diff', type='float', default=None,
help=('maxDiff to consider a match (applicable for -m bwa-short) -- '
'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]"),
]
script_info['version'] = __version__
def main():
# Parse the command line parameters
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
# Create local copies of the options to avoid repetitive lookups
assignment_method = opts.assignment_method
refseqs_fp = abspath(opts.refseqs_fp)
input_seqs_filepath = abspath(opts.input_seqs_filepath)
verbose = opts.verbose
# use the otu_picking_method value to get the otu picker constructor
assignment_function = assignment_functions[assignment_method]
# create the output directory name (if not provided) and
# create it if it doesn't already exist
output_dir = abspath(opts.output_dir or assignment_method + '_mapped')
create_dir(output_dir, fail_on_exist=False)
if assignment_method == 'usearch':
assignment_function(query_fp=input_seqs_filepath,
refseqs_fp=refseqs_fp,
output_dir=output_dir,
evalue=opts.evalue,
min_id=opts.min_percent_id,
queryalnfract=opts.queryalnfract,
targetalnfract=opts.targetalnfract,
maxaccepts=opts.max_accepts,
maxrejects=opts.max_rejects,
observation_metadata_fp=opts.observation_metadata_fp,
HALT_EXEC=False)
elif assignment_method == 'blat-nt':
assignment_function(query_fp=input_seqs_filepath,
refseqs_fp=refseqs_fp,
output_dir=output_dir,
evalue=opts.evalue,
min_id=opts.min_percent_id,
observation_metadata_fp=opts.observation_metadata_fp,
HALT_EXEC=False)
elif assignment_method == 'blat':
assignment_function(query_fp=input_seqs_filepath,
refseqs_fp=refseqs_fp,
output_dir=output_dir,
evalue=opts.evalue,
min_id=opts.min_percent_id,
genetic_code=opts.genetic_code,
observation_metadata_fp=opts.observation_metadata_fp,
HALT_EXEC=False)
elif assignment_method == 'bwa-sw':
assignment_function(query_fp=input_seqs_filepath,
refseqs_fp=refseqs_fp,
output_dir=output_dir,
observation_metadata_fp=opts.observation_metadata_fp,
HALT_EXEC=False)
elif assignment_method == 'bwa-short':
# cast max_diff to an int if it's being passed as an int
if opts.max_diff != None and opts.max_diff > 1.0:
max_diff = int(opts.max_diff)
else:
max_diff = opts.max_diff
assignment_function(query_fp=input_seqs_filepath,
refseqs_fp=refseqs_fp,
output_dir=output_dir,
max_diff=max_diff,
observation_metadata_fp=opts.observation_metadata_fp,
HALT_EXEC=True)
else:
## other -- shouldn't be able to get here as a KeyError would have
## been raised earlier
raise ValueError, "Unknown read mapping method: %s" % assignment_method
if __name__ == "__main__":
main()
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