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#cython: language_level=3
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.dms import DMS
from obitools3.dms.view.view cimport View, Line_selection
from obitools3.uri.decode import open_uri
from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption, addNoProgressBarOption
from obitools3.dms.view import RollbackException
from obitools3.apps.config import logger
from obitools3.utils cimport tobytes
import sys
from cpython.exc cimport PyErr_CheckSignals
__title__="Split"
def addOptions(parser):
addMinimalInputOption(parser)
addNoProgressBarOption(parser)
group=parser.add_argument_group("obi split specific options")
group.add_argument('-p','--prefix',
action="store", dest="split:prefix",
metavar="<PREFIX>",
help="Prefix added to each subview name (included undefined)")
group.add_argument('-t','--tag-name',
action="store", dest="split:tagname",
metavar="<TAG_NAME>",
help="Attribute/tag used to split the input")
group.add_argument('-u','--undefined',
action="store", dest="split:undefined",
default=b'UNDEFINED',
metavar="<VIEW_NAME>",
help="Name of the view where undefined sequenced are stored (will be PREFIX_VIEW_NAME)")
def run(config):
DMS.obi_atexit()
logger("info", "obi split")
# Open the input
input = open_uri(config["obi"]["inputURI"])
if input is None:
raise Exception("Could not read input view")
i_dms = input[0]
i_view = input[1]
# Initialize the progress bar
if config['obi']['noprogressbar'] == False:
pb = ProgressBar(len(i_view), config)
else:
pb = None
tag_to_split = config["split"]["tagname"]
undefined = tobytes(config["split"]["undefined"])
selections = {}
# Go through input view and split
for i in range(len(i_view)):
PyErr_CheckSignals()
if pb is not None:
pb(i)
line = i_view[i]
if tag_to_split not in line or line[tag_to_split] is None or len(line[tag_to_split])==0:
value = undefined
else:
value = line[tag_to_split]
if value not in selections:
selections[value] = Line_selection(i_view)
selections[value].append(i)
if pb is not None:
pb(len(i_view), force=True)
print("", file=sys.stderr)
# Create output views with the line selection
try:
for cat in selections:
o_view_name = config["split"]["prefix"].encode()+cat
o_view = selections[cat].materialize(o_view_name)
# Save command config in View and DMS comments
command_line = " ".join(sys.argv[1:])
input_dms_name=[input[0].name]
input_view_name=[input[1].name]
if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
o_view.write_config(config, "split", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
o_view.close()
except Exception, e:
raise RollbackException("obi split error, rollbacking view: "+str(e), o_view)
i_dms.record_command_line(command_line)
i_dms.close(force=True)
logger("info", "Done.")
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