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All commands now handle outputing to another DMS + small fixes

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This commit is contained in:
Celine Mercier
2018-11-02 19:03:09 +01:00
parent 8a8e9e50b2
commit 35f3e7c30b
10 changed files with 266 additions and 153 deletions
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70
python/obitools3/commands/clean.pyx Normal file → Executable file
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@ -8,7 +8,7 @@ from obitools3.dms.capi.obiclean cimport obi_clean
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
from obitools3.uri.decode import open_uri
from obitools3.apps.config import logger
from obitools3.utils cimport tobytes
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
@ -66,38 +66,58 @@ def run(config):
DMS.obi_atexit()
logger("info", "obi clean")
# Open DMS
dms_name = config['obi']['inputURI'].split('/')[0]
dms = open_uri(dms_name)[0]
# Read the name of the input view
uri_i = config['obi']['inputURI'].split('/')
i_view_name = uri_i[1]
# Read the name of the output view
uri_o = config['obi']['outputURI'].split('/')
if len(uri_o)==2:
# Check that input and output DMS are the same (predicate, to discuss)
if dms_name != uri_o[0]:
raise Exception("Input and output DMS must be the same")
o_view_name = uri_o[1]
# 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, run obiclean 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 = uri_o[0]
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=[dms_name], input_view_name=[i_view_name])
comments = View.print_config(config, "clean", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name])
if obi_clean(tobytes(dms_name), tobytes(i_view_name), tobytes(config['clean']['sample-tag-name']), tobytes(o_view_name), comments, \
if obi_clean(tobytes(i_dms_name), 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'], 1) < 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)
# Save command config in DMS comments
dms.record_command_line(command_line)
o_dms.record_command_line(command_line)
print("\n")
print(repr(dms[o_view_name]))
dms.close()
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()