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"""
Command line object for HHfilter Multiple Sequence Alignment filtering application
"""
__author__ = "Felix Simkovic"
__date__ = "05 Aug 2016"
__version__ = "0.13.3"
from Bio.Application import _Option
from Bio.Application import AbstractCommandline
[docs]class HHfilterCommandline(AbstractCommandline):
"""
Command line object for HHfilter [#]_ [#]_ alignment filter application
https://toolkit.tuebingen.mpg.de/hhfilter
Filter an alignment by maximum sequence identity of match states and minimum coverage.
.. [#] Alva V., Nam SZ., Söding J., Lupas AN. (2016). The MPI bioinformatics Toolkit as an
integrative platform for advanced protein sequence and structure analysis. Nucleic Acids Res. pii: gkw348.
.. [#] Remmert M., Biegert A., Hauser A., Söding J. (2011). HHblits: Lightning-fast iterative
protein sequence searching by HMM-HMM alignment. Nat Methods. 9(2):173-5.
Examples
--------
To generate a Multiple Sequence Alignment, use:
>>> from conkit.applications import HHfilterCommandline
>>> hhfilter_cline = HHfilterCommandline(
... input='test.a3m', output='test.filtered.a3m'
... )
>>> print(hhfilter_cline)
hhfilter -i test.a3m -o test.filtered.a3m
You would typically run the command line with :func:`hhfilter_cline` or via
the :mod:`~subprocess` module.
"""
def __init__(self, cmd="hhfilter", **kwargs):
self.parameters = [
_Option(
["-i", "input"],
"read input file in A3M/A2M or FASTA format",
filename=True,
is_required=True,
equate=False,
),
_Option(
["-o", "output"], "write to output file in A3M format", filename=True, is_required=True, equate=False
),
_Option(["-a", "append_output"], "append to output file in A3M format", filename=True, equate=False),
# Options
_Option(
["-v", "verbose"],
"verbose mode: 0:no screen output 1:only warings 2: verbose [default: 2]",
equate=False,
),
_Option(["-id", "pairwise_identity"], "maximum pairwise sequence identity [default: 90]", equate=False),
_Option(
["-diff", "diversity"],
"filter MSAs by selecting most diverse set of sequences, keeping "
"at least this many seqs in each MSA block of length 50 [default: 1000]",
equate=False,
),
_Option(["-cov", "coverage"], "minimum coverage with master sequence (%) [default: 0]", equate=False),
_Option(
["-qid", "query_identity"],
"minimum sequence identity with master sequence (%) [default: 0]",
equate=False,
),
_Option(
["-qsc", "per_column_score"],
"minimum score per column with master sequence [default: -20.0]",
equate=False,
),
_Option(
["-neff", "nr_effective_sequences"],
"target diversity of multiple sequence alignment [default: off]",
equate=False,
),
# # Input alignment options
# _Option(['-M', 'a2m'],
# 'use A2M/A3M input alignment format',
# equate=False),
# _Option(['-M', 'fasta'],
# 'use FASTA input alignment format',
# equate=False),
# _Option(['-M', 'match_states'],
# 'use FASTA: columns with fewer than X% gaprs are match states',
# equate=False),
]
AbstractCommandline.__init__(self, cmd, **kwargs)
