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"""
Command line object for HHblits Multiple Sequence Alignment application
"""
__author__ = "Felix Simkovic"
__date__ = "05 Aug 2016"
__version__ = "0.13.3"
from Bio.Application import _Option
from Bio.Application import _Switch
from Bio.Application import AbstractCommandline
[docs]class HHblitsCommandline(AbstractCommandline):
"""
Command line object for HHblits [#]_ [#]_ alignment generation
https://toolkit.tuebingen.mpg.de/hhblits
The HHblits program is a homology detection tool by iterative HMM-HMM comparison.
.. [#] 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 HHblitsCommandline
>>> hhblits_cline = HHblitsCommandline(
... input="test.fasta", database="uniprot20_29Feb2012"
... )
>>> print(hhblits_cline)
hhblits -i test.fasta -d uniprot20_29Feb2012
You would typically run the command line with :func:`hhblits_cline` or via
the :mod:`~subprocess` module.
"""
def __init__(self, cmd="hhblits", **kwargs):
# TODO: Figure out how to do mutual groups
if "local" in list(kwargs.keys()) and "global" in list(kwargs.keys()):
raise ValueError('Use only one of "global_aln/local_aln" alignment modes')
self.parameters = [
_Option(
["-i", "input"],
"single sequence or multiple sequence alignment in " "a3m, a2m, or FASTA format, or HMM in hmm format",
filename=True,
is_required=True,
equate=False,
),
# Options
_Option(["-d", "database"], "database name (e.g. uniprot20_29Feb2012)", is_required=True, equate=False),
_Option(["-n", "niterations"], "number of iterations [default: 2]", equate=False),
_Option(
["-e", "evalue"], "E-value cutoff for inclusion in result alignment [default: 0.001]", 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),
# Output options
_Option(
["-o", "output"],
"write results in standard format to file [default: <infile.hhr>]",
filename=True,
equate=False,
),
_Option(
["-oa3m", "oa3m"],
"write result MSA with significant matches in a3m format",
filename=True,
equate=False,
),
_Option(
["-ohhm", "ohhm"],
"write result MSA with significant matches in hmm format",
filename=True,
equate=False,
),
_Option(
["-opsi", "opsi"],
"write result MSA with significant matches in psi format",
filename=True,
equate=False,
),
_Option(["-oalis", "oalis"], "write MSAs in A3M format after each iteration", filename=True, equate=False),
# Filter options applied to query MSA, database MSAs, and result MSA
_Switch(["-all", "show_all"], "show all sequences in result MSA; do not filter result MSA"),
_Option(["-id", "id"], "maximum pairwise sequence identity [default: 90]", equate=False),
_Option(
["-diff", "diff"],
"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", "cov"], "minimum coverage with master sequence (%) [default: 0]", equate=False),
_Option(["-qid", "qid"], "minimum sequence identity with master sequence (%) [default: 0]", equate=False),
_Option(["-qsc", "qsc"], "minimum score per column with master sequence [default: -20.0]", equate=False),
_Option(["-neff", "neff"], "target diversity of multiple sequence alignment [default: off]", equate=False),
# HMM-HMM alignment options
_Switch(["-norealign", "norealign"], "do NOT realign displayed hits with MAC algorithm [default: realign]"),
_Option(
["-mact", "mac_realignment_threshold"],
"posterior probability threshold for MAC re-alignment [default: 0.350], "
"Parameter controls alignment greediness: 0:global >0.1:local",
equate=False,
),
_Switch(["-glob", "global_aln"], "use global alignment mode for searching/ranking [default: local]"),
_Switch(["-loc", "loca_alnl"], "use local alignment mode for searching/ranking [default: local]"),
# Other options
_Option(
["-v", "verbose"],
"verbose mode: 0:no screen output 1:only warings 2: verbose [default: 2]",
equate=False,
),
_Option(
["-neffmax", "neffmax"],
"skip further search iterations when diversity Neff of query "
"MSA becomes larger than neffmax [default: 10.0]",
equate=False,
),
_Option(["-cpu", "cpu"], "number of CPUs to use (for shared memory SMPs) [default: 2]"),
# Extra options from `-h all`
_Option(
["-maxfilt", "maxfilt"],
"max number of hits allowed to pass 2nd prefilter (default=20000)",
equate=False,
),
]
AbstractCommandline.__init__(self, cmd, **kwargs)
