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map_reads_to_reference.py
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map_reads_to_reference.py
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#!/usr/bin/env python
# File created on 13 Jul 2012
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
from os.path import join, splitext, exists
from bfillings.blat import MinimalBlatParser9
from bfillings.blat import (assign_dna_reads_to_protein_database
as blat_assign_dna_reads_to_protein_database,
assign_dna_reads_to_dna_database
as blat_assign_dna_reads_to_dna_database)
from bfillings.usearch import (clusters_from_blast_uc_file,
assign_dna_reads_to_database
as usearch_assign_dna_reads_to_database)
from bfillings.bwa import (assign_dna_reads_to_dna_database
as bwa_assign_dna_reads_to_dna_database)
from qiime.format import format_observation_map
from qiime.parse import parse_taxonomy, MinimalSamParser
from qiime.make_otu_table import make_otu_table
from qiime.util import get_qiime_temp_dir, create_dir, write_biom_table
class DatabaseMapper(object):
def __call__(self,
query_fasta_fp,
database_fasta_fp,
output_dir,
observation_metadata_fp=None,
params=None,
HALT_EXEC=False):
if params is None:
params = {}
""" Call the DatabaseMapper """
create_dir(output_dir)
raw_output_fp = self._get_raw_output_fp(output_dir,
params)
output_observation_map_fp = '%s/observation_map.txt' % output_dir
output_biom_fp = '%s/observation_table.biom' % output_dir
log_fp = '%s/observation_table.log' % output_dir
self._assign_dna_reads_to_database(
query_fasta_fp=query_fasta_fp,
database_fasta_fp=database_fasta_fp,
raw_output_fp=raw_output_fp,
temp_dir=get_qiime_temp_dir(),
params=params,
HALT_EXEC=HALT_EXEC)
self._process_raw_output(raw_output_fp,
log_fp,
output_observation_map_fp)
self._generate_biom_output(output_observation_map_fp,
output_biom_fp,
observation_metadata_fp)
def _generate_biom_output(self,
observation_map_fp,
output_biom_fp,
observation_metadata_fp):
if observation_metadata_fp is not None:
observation_metadata = \
parse_taxonomy(open(observation_metadata_fp, 'U'))
else:
observation_metadata = None
biom_table = make_otu_table(open(observation_map_fp, 'U'),
observation_metadata)
write_biom_table(biom_table, output_biom_fp)
def _assign_dna_reads_to_database(self,
query_fasta_fp,
database_fasta_fp,
raw_output_fp,
observation_metadata_fp,
params,
HALT_EXEC):
raise NotImplementedError(
"DatabaseMapper subclasses must override _assign_dna_reads_to_database")
def _get_raw_output_fp(self, output_dir, params):
""" Generate filepath for raw output
subclasses will generally want to override this method
"""
return join(output_dir, 'raw_output.txt')
def _process_raw_output(self,
raw_output_fp,
log_fp,
output_observation_map_fp):
raise NotImplementedError(
"DatabaseMapper subclasses must override _process_raw_output")
class UsearchDatabaseMapper(DatabaseMapper):
def _assign_dna_reads_to_database(self,
query_fasta_fp,
database_fasta_fp,
raw_output_fp,
temp_dir,
params,
HALT_EXEC):
usearch_assign_dna_reads_to_database(
query_fasta_fp=query_fasta_fp,
database_fasta_fp=database_fasta_fp,
output_fp=raw_output_fp,
temp_dir=temp_dir,
params=params,
HALT_EXEC=HALT_EXEC)
def _get_raw_output_fp(self,
output_dir,
params):
""" Generate filepath for .uc file """
return join(output_dir, 'out.uc')
def _process_raw_output(self,
raw_output_fp,
log_fp,
output_observation_map_fp):
""" Generate observation map and biom table from .uc file
"""
hits, failures = clusters_from_blast_uc_file(
open(raw_output_fp, 'U'), 9)
observation_map_f = open(output_observation_map_fp, 'w')
for line in format_observation_map(hits.items(), ''):
observation_map_f.write(line)
observation_map_f.close()
class BlatDatabaseMapper(DatabaseMapper):
MaxEvalue = 1e-10
MinId = 0.97
def _get_raw_output_fp(self,
output_dir,
params):
""" Generate filepath for .bl9 (blast9) file """
return join(output_dir, 'out.bl9')
def _process_raw_output(self,
raw_output_fp,
log_fp,
output_observation_map_fp):
""" Generate observation map and biom table from .bl9 file
"""
result = {}
pct_id_field = 2
evalue_field = 10
output_observation_map_f = open(output_observation_map_fp, 'w')
log_f = open(log_fp, 'w')
for summary, blat_results in MinimalBlatParser9(
open(raw_output_fp, 'U'),
include_column_names=False):
for e in blat_results:
if (float(e[evalue_field]) <= self.MaxEvalue and
float(e[pct_id_field]) / 100. >= self.MinId):
query_id = e[0]
subject_id = e[1]
try:
result[subject_id].append(query_id)
except KeyError:
result[subject_id] = [query_id]
log_f.write('\t'.join(e))
log_f.write('\n')
break
log_f.close()
for e in result.items():
output_observation_map_f.write(
'%s\t%s\n' %
(e[0], '\t'.join(e[1])))
output_observation_map_f.close()
return result
def _assign_dna_reads_to_database(self,
query_fasta_fp,
database_fasta_fp,
raw_output_fp,
temp_dir,
params,
HALT_EXEC):
blat_assign_dna_reads_to_protein_database(
query_fasta_fp=query_fasta_fp,
database_fasta_fp=database_fasta_fp,
output_fp=raw_output_fp,
temp_dir=temp_dir,
params=params)
class BlatNtDatabaseMapper(BlatDatabaseMapper):
def _assign_dna_reads_to_database(self,
query_fasta_fp,
database_fasta_fp,
raw_output_fp,
temp_dir,
params,
HALT_EXEC):
blat_assign_dna_reads_to_dna_database(
query_fasta_fp=query_fasta_fp,
database_fasta_fp=database_fasta_fp,
output_fp=raw_output_fp,
params=params)
class BwaSwDatabaseMapper(DatabaseMapper):
def _get_raw_output_fp(self,
output_dir,
params):
""" Generate filepath for .bl9 (blast9) file """
return join(output_dir, 'bwa_raw_out.sam')
def _process_raw_output(self,
raw_output_fp,
log_fp,
output_observation_map_fp):
""" Generate observation map and biom table from .bl9 file
"""
result = {}
query_id_field = 0
flag_field = 1
subject_id_field = 2
output_observation_map_f = open(output_observation_map_fp, 'w')
log_f = open(log_fp, 'w')
for e in MinimalSamParser(open(raw_output_fp, 'U')):
query_id = e[query_id_field]
subject_id = e[subject_id_field]
flag = int(e[flag_field])
if (flag != 4):
try:
result[subject_id].append(query_id)
except KeyError:
result[subject_id] = [query_id]
log_f.write('\t'.join(e))
log_f.write('\n')
log_f.close()
for e in result.items():
output_observation_map_f.write(
'%s\t%s\n' %
(e[0], '\t'.join(e[1])))
output_observation_map_f.close()
return result
def _assign_dna_reads_to_database(self,
query_fasta_fp,
database_fasta_fp,
raw_output_fp,
temp_dir,
params,
HALT_EXEC):
_params = {}
_params.update(params)
bwa_assign_dna_reads_to_dna_database(
query_fasta_fp=query_fasta_fp,
database_fasta_fp=database_fasta_fp,
out_fp=raw_output_fp,
params=_params)
class BwaShortDatabaseMapper(BwaSwDatabaseMapper):
def _assign_dna_reads_to_database(self,
query_fasta_fp,
database_fasta_fp,
raw_output_fp,
temp_dir,
params,
HALT_EXEC):
_aln_params = {'-f': splitext(raw_output_fp)[0] + '.sai'}
if 'aln_params' in params:
_aln_params.update(params['aln_params'])
params['algorithm'] = 'bwa-short'
params['aln_params'] = _aln_params
bwa_assign_dna_reads_to_dna_database(
query_fasta_fp=query_fasta_fp,
database_fasta_fp=database_fasta_fp,
out_fp=raw_output_fp,
params=params)
def usearch_database_mapper(query_fp,
refseqs_fp,
output_dir,
evalue,
min_id,
queryalnfract,
targetalnfract,
maxaccepts,
maxrejects,
observation_metadata_fp=None,
HALT_EXEC=False):
params = {}
params['--evalue'] = evalue
params['--id'] = min_id
params['--queryalnfract'] = queryalnfract
params['--targetalnfract'] = targetalnfract
params['--maxaccepts'] = maxaccepts
params['--maxrejects'] = maxrejects
usearch_db_mapper = UsearchDatabaseMapper()
usearch_db_mapper(query_fp,
refseqs_fp,
output_dir,
params=params,
observation_metadata_fp=observation_metadata_fp,
HALT_EXEC=HALT_EXEC)
def blat_database_mapper(query_fp,
refseqs_fp,
output_dir,
evalue,
min_id,
genetic_code,
observation_metadata_fp=None,
HALT_EXEC=False):
params = {'-minIdentity': min_id,
'genetic_code': genetic_code}
blat_db_mapper = BlatDatabaseMapper()
blat_db_mapper.MinId = min_id
blat_db_mapper.MaxEvalue = evalue
blat_db_mapper(query_fp,
refseqs_fp,
output_dir,
params=params,
observation_metadata_fp=observation_metadata_fp,
HALT_EXEC=HALT_EXEC)
def blat_nt_database_mapper(query_fp,
refseqs_fp,
output_dir,
evalue,
min_id,
observation_metadata_fp=None,
HALT_EXEC=False):
params = {'-minIdentity': min_id}
blat_db_mapper = BlatNtDatabaseMapper()
blat_db_mapper.MinId = min_id
blat_db_mapper.MaxEvalue = evalue
blat_db_mapper(query_fp,
refseqs_fp,
output_dir,
params=params,
observation_metadata_fp=observation_metadata_fp,
HALT_EXEC=HALT_EXEC)
def bwa_sw_database_mapper(query_fp,
refseqs_fp,
output_dir,
observation_metadata_fp=None,
HALT_EXEC=False):
bwa_db_mapper = BwaSwDatabaseMapper()
params = {}
bwa_db_mapper(query_fp,
refseqs_fp,
output_dir,
params=params,
observation_metadata_fp=observation_metadata_fp,
HALT_EXEC=HALT_EXEC)
def bwa_short_database_mapper(query_fp,
refseqs_fp,
output_dir,
max_diff,
observation_metadata_fp=None,
HALT_EXEC=False):
bwa_db_mapper = BwaShortDatabaseMapper()
if max_diff is not None:
params = {'aln_params': {'-n': max_diff}}
else:
params = {}
bwa_db_mapper(query_fp,
refseqs_fp,
output_dir,
params=params,
observation_metadata_fp=observation_metadata_fp,
HALT_EXEC=HALT_EXEC)