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Python: made all commands handle output to buffer object (e.g. stdout)

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This commit is contained in:
Celine Mercier
2020-07-24 16:09:48 +02:00
parent 46ca693ca9
commit 8aa455ad8a
18 changed files with 511 additions and 213 deletions
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8
python/obitools3/commands/import.pyx
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@ -47,6 +47,8 @@ from obitools3.apps.config import logger
from cpython.exc cimport PyErr_CheckSignals
from io import BufferedWriter
__title__="Imports sequences from different formats into a DMS"
@ -130,7 +132,7 @@ def run(config):
if entry_count > 0:
logger("info", "Importing %d entries", entry_count)
else:
logger("info", "Importing an unknow number of entries")
logger("info", "Importing an unknown number of entries")
# TODO a bit dirty?
if input[2]==Nuc_Seq or input[2]==View_NUC_SEQS:
@ -178,7 +180,7 @@ def run(config):
return
if entry_count >= 0:
pb = ProgressBar(entry_count, config, seconde=5)
pb = ProgressBar(entry_count, config)
NUC_SEQS_view = False
if isinstance(output[1], View) :
@ -243,7 +245,7 @@ def run(config):
if isinstance(input[0], CompressedFile):
input_is_file = True
if entry_count >= 0:
pb = ProgressBar(entry_count, config, seconde=5)
pb = ProgressBar(entry_count, config)
try:
input[0].close()
except AttributeError: