# coding=utf-8
"""
Command line object for HHfilter Multiple Sequence Alignment filtering application
"""
__author__ = "Felix Simkovic"
__date__ = "05 Aug 2016"
__version__ = 0.1
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 Python 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)
