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Commands: updated for JSON formatted comments with history

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This commit is contained in:
Celine Mercier
2018-10-07 19:10:34 +02:00
parent 35cf2962cc
commit e9a41c5b97
11 changed files with 144 additions and 34 deletions
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15
python/obitools3/commands/clean.pyx
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@ -9,9 +9,11 @@ from obitools3.apps.optiongroups import addSequenceInputOption, addMinimalOutput
from obitools3.uri.decode import open_uri
from obitools3.apps.config import logger
from obitools3.utils cimport tobytes
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"
@ -82,11 +84,18 @@ def run(config):
o_view_name = uri_o[1]
else:
o_view_name = uri_o[0]
if obi_clean(tobytes(dms_name), tobytes(i_view_name), tobytes(config['clean']['sample-tag-name']), tobytes(o_view_name), b"obiclean", \
# 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])
if obi_clean(tobytes(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")
# Save command config in DMS comments
dms.record_command_line(command_line)
print("\n")
print(repr(dms[o_view_name]))