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#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.obiclean cimport obi_clean
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addNoProgressBarOption
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
from io import BufferedWriter
import sys
__title__="Tag a set of sequences for PCR and sequencing errors identification"
def addOptions(parser):
addMinimalInputOption(parser)
addMinimalOutputOption(parser)
addNoProgressBarOption(parser)
group = parser.add_argument_group('obi clean specific options')
group.add_argument('--distance', '-d',
action="store", dest="clean:distance",
metavar='<DISTANCE>',
default=1.0,
type=float,
help="Maximum numbers of errors between two variant sequences. Default: 1.")
group.add_argument('--sample-tag', '-s',
action="store",
dest="clean:sample-tag-name",
metavar="<SAMPLE TAG NAME>",
type=str,
help="Name of the tag where merged sample count informations are kept (typically generated by obi uniq, usually MERGED_sample, default: None).")
group.add_argument('--ratio', '-r',
action="store", dest="clean:ratio",
metavar='<RATIO>',
default=0.5,
type=float,
help="Maximum ratio between the counts of two sequences so that the less abundant one can be considered"
" a variant of the more abundant one. Default: 0.5.")
group.add_argument('--heads-only', '-H',
action="store_true",
dest="clean:heads-only",
default=False,
help="Only sequences labeled as heads are kept in the output. Default: False")
# group.add_argument('--cluster-tags', '-C',
# action="store_true",
# dest="clean:cluster-tags",
# default=False,
# help="Adds tags for each sequence giving its cluster's head and weight for each sample.")
group.add_argument('--thread-count','-p', # TODO should probably be in a specific option group
action="store", dest="clean:thread-count",
metavar='<THREAD COUNT>',
default=-1,
type=int,
help="Number of threads to use for the computation. Default: the maximum available.")
def run(config):
DMS.obi_atexit()
logger("info", "obi clean")
# 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]
output_0 = output[0]
final_o_view_name = output[1]
# If stdout output or the input and output DMS are not the same, create a temporary view that will be exported to
# the right DMS and deleted in the other afterwards.
if i_dms != o_dms or type(output_0)==BufferedWriter:
temporary_view_name = b"temp"
i=0
while temporary_view_name in i_dms: # Making sure view name is unique in input DMS
temporary_view_name = temporary_view_name+b"_"+str2bytes(str(i))
i+=1
o_view_name = temporary_view_name
if type(output_0)==BufferedWriter:
o_dms = i_dms
else:
o_view_name = final_o_view_name
# Save command config in View comments
command_line = " ".join(sys.argv[1:])
comments = View.print_config(config, "clean", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name])
if 'sample-tag-name' not in config['clean']:
config['clean']['sample-tag-name'] = ""
if obi_clean(i_dms.name_with_full_path, tobytes(i_view_name), tobytes(config['clean']['sample-tag-name']), tobytes(o_view_name), comments, \
config['clean']['distance'], config['clean']['ratio'], config['clean']['heads-only'], config['clean']['thread-count']) < 0:
raise Exception("Error running obiclean")
# 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)
# stdout output: write to buffer
if type(output_0)==BufferedWriter:
logger("info", "Printing to output...")
o_view = o_dms[o_view_name]
o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
o_view.close()
# Save command config in DMS comments
o_dms.record_command_line(command_line)
#print("\n\nOutput view:\n````````````", file=sys.stderr)
#print(repr(o_dms[final_o_view_name]), file=sys.stderr)
# If the input and the output DMS are different or if stdout output, delete the temporary imported view used to create the final view
if i_dms != o_dms or type(output_0)==BufferedWriter:
View.delete_view(i_dms, o_view_name)
o_dms.close(force=True)
i_dms.close(force=True)
logger("info", "Done.")
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