Commit ece942e7 authored by Celine Mercier's avatar Celine Mercier

new command: build_ref_db to build a reference database with metadata

for the taxonomic assignment of sequences
parent ef8dc85f
#cython: language_level=3
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.dms.dms cimport DMS
from obitools3.dms.view import RollbackException
from obitools3.dms.capi.build_reference_db cimport build_reference_db
from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption
from obitools3.uri.decode import open_uri
from obitools3.apps.config import logger
from obitools3.utils cimport tobytes, str2bytes
from obitools3.dms.view.view cimport View
from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
import sys
__title__="Tag a set of sequences for PCR and sequencing errors identification"
def addOptions(parser):
addMinimalInputOption(parser)
addTaxonomyOption(parser)
addMinimalOutputOption(parser)
group = parser.add_argument_group('obi build_ref_db specific options')
group.add_argument('--threshold','-t',
action="store", dest="build_ref_db:threshold",
metavar='<THRESHOLD>',
default=0.0,
type=float,
help="Score threshold as a normalized identity, e.g. 0.95 for an identity of 95%%. Default: 0.00"
" (no threshold).")
def run(config):
DMS.obi_atexit()
logger("info", "obi build_ref_db")
# Open the input: only the DMS
input = open_uri(config['obi']['inputURI'],
dms_only=True)
if input is None:
raise Exception("Could not read input")
i_dms = input[0]
i_dms_name = input[0].name
i_view_name = input[1]
# Open the output: only the DMS
output = open_uri(config['obi']['outputURI'],
input=False,
dms_only=True)
if output is None:
raise Exception("Could not create output")
o_dms = output[0]
final_o_view_name = output[1]
# If the input and output DMS are not the same, build the database creating a temporary view that will be exported to
# the right DMS and deleted in the other afterwards.
if i_dms != o_dms:
temporary_view_name = final_o_view_name
i=0
while temporary_view_name in i_dms: # Making sure view name is unique in input DMS
temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
i+=1
o_view_name = temporary_view_name
else:
o_view_name = final_o_view_name
# Read taxonomy name
taxonomy_name = config['obi']['taxoURI'].split("/")[-1] # Robust in theory
# Save command config in View comments
command_line = " ".join(sys.argv[1:])
comments = View.print_config(config, "build_ref_db", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name])
if build_reference_db(tobytes(i_dms_name), tobytes(i_view_name), tobytes(taxonomy_name), tobytes(o_view_name), comments, config['build_ref_db']['threshold']) < 0:
raise Exception("Error building a reference database")
# If the input and output DMS are not the same, export result view to output DMS
if i_dms != o_dms:
View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
# Save command config in DMS comments
o_dms.record_command_line(command_line)
print("\n")
print(repr(o_dms[final_o_view_name]))
# If the input and the output DMS are different, delete the temporary result view in the input DMS
if i_dms != o_dms:
View.delete_view(i_dms, o_view_name)
o_dms.close()
i_dms.close()
../../../src/array_indexer.c
../../../src/bloom.c
../../../src/build_reference_db.c
../../../src/char_str_indexer.c
../../../src/crc64.c
../../../src/dna_seq_indexer.c
......
../../src/array_indexer.c
../../src/bloom.c
../../src/build_reference_db.c
../../src/char_str_indexer.c
../../src/crc64.c
../../src/dna_seq_indexer.c
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment