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import: now imports and adds taxids for SILVA and RDP files, added

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import of lists, fixed skipping of errors (was not overwriting), and
fixed --no-progress-bar option
This commit is contained in:
mercierc
2021-06-01 09:21:07 +12:00
parent c2f3d90dc1
commit 3e45c34491
4 changed files with 122 additions and 41 deletions
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8
python/obitools3/apps/optiongroups/__init__.py
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@ -49,7 +49,13 @@ def __addImportInputOption(optionManager):
action="store_const", dest="obi:inputformat",
default=None,
const=b'silva',
help="Input file is in SILVA fasta format")
help="Input file is in SILVA fasta format. If NCBI taxonomy provided with --taxonomy, taxid and scientific name will be added for each sequence.")
group.add_argument('--rdp-input',
action="store_const", dest="obi:inputformat",
default=None,
const=b'rdp',
help="Input file is in RDP training set fasta format. If NCBI taxonomy provided with --taxonomy, taxid and scientific name will be added for each sequence.")
group.add_argument('--embl-input',
action="store_const", dest="obi:inputformat",