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|
Sequence record editing options
-------------------------------
.. cmdoption:: --seq-rank
Adds a new attribute named ``seq_rank`` to the sequence record indicating
its entry number in the sequence file.
.. cmdoption:: -R <OLD_NAME>:<NEW_NAME>, --rename-tag=<OLD_NAME>:<NEW_NAME>
Changes attribute name <OLD_NAME> to <NEW_NAME>. When attribute
named <OLD_NAME> is missing, the sequence record is
skipped and the next one is examined.
.. cmdoption:: --delete-tag=<KEY>
Deletes attribute named <ATTRIBUTE_NAME>.When this attribute
is missing, the sequence record is skipped and the
next one is examined.
.. cmdoption:: -S <KEY>:<PYTHON_EXPRESSION>, --set-tag=<KEY>:<PYTHON_EXPRESSION>
Creates a new attribute named with a key <KEY> and a
value computed from <PYTHON_EXPRESSION>.
.. cmdoption:: --tag-list=<FILENAME>
<FILENAME> points to a file containing attribute
names and values to modify for specified sequence records.
.. cmdoption:: --set-identifier=<PYTHON_EXPRESSION>
Sets sequence record identifier with a value computed
from <PYTHON_EXPRESSION>.
.. cmdoption:: --run=<PYTHON_EXPRESSION>
Runs a python expression on each selected sequence.
.. cmdoption:: --set-sequence=<PYTHON_EXPRESSION>
Changes the sequence itself with a value computed from
<PYTHON_EXPRESSION>.
.. cmdoption:: -T, --set-definition=<PYTHON_EXPRESSION>
Sets sequence definition with a value computed from
<PYTHON_EXPRESSION>.
.. cmdoption:: -O, --only-valid-python
Allows only valid python expressions.
.. cmdoption:: -C, --clear
Clears all attributes associated to the sequence records.
.. cmdoption:: -k <KEY>, --keep=<KEY>
Keeps only attribute with key <KEY>. Several ``-k``
options can be combined.
.. cmdoption:: --length
Adds attribute with ``seq_length`` as a key and sequence length as a value.
.. cmdoption:: --with-taxon-at-rank=<RANK_NAME>
Adds taxonomic annotation at taxonomic rank
<RANK_NAME>.
.. cmdoption:: -m <MCLFILE>, --mcl=<MCLFILE>
Creates a new attribute containing the number of the
cluster the sequence record was assigned to, as
indicated in file <MCLFILE>.
.. cmdoption:: --uniq-id
Forces sequence record ids to be unique.
|
