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"""
Command line object for CCMpred contact prediction application
"""
__author__ = "Felix Simkovic"
__date__ = "04 Aug 2016"
__version__ = "0.1"
from Bio.Application import _Option
from Bio.Application import AbstractCommandline
[docs]class CdhitCommandline(AbstractCommandline):
"""
Command line object for Cd-hit [#]_ [#]_
http://cd-hit.org
CD-HIT is a very widely used program for clustering and comparing
protein or nucleotide sequences. CD-HIT was originally developed
by Dr. Weizhong Li at Dr. Adam Godzik's Lab at the Burnham Institute
(now Sanford-Burnham Medical Research Institute).
CD-HIT is very fast and can handle extremely large databases. CD-HIT
helps to significantly reduce the computational and manual efforts in
many sequence analysis tasks and aids in understanding the data
structure and correct the bias within a dataset.
.. [#] Li W, Jaroszewski L, Godzik A(2001). Clustering of highly homologous sequences
to reduce thesize of large protein database. Bioinformatics 17, 282-283.
.. [#] Li W, Jaroszewski L, Godzik A (2002). Tolerating some redundancy significantly
speeds up clustering of large protein databases. Bioinformatics 18, 77-82.
Examples
--------
>>> from conkit.applications import CdhitCommandline
>>> cdhit_cline = CdhitCommandline()
>>> print(cdhit_cline)
You would typically run the command line with :func:`cdhit_cline` or via
the Python subprocess module.
"""
def __init__(self, cmd="cd-hit", **kwargs):
self.parameters = [
_Option(['-i', 'input'],
'input filename in fasta format, required',
filename=True,
equate=False,
is_required=True),
_Option(['-o', 'output'],
'output filename, required',
filename=True,
equate=False,
is_required=True),
_Option(['-c', 'seq_id_thres'],
"sequence identity threshold, default 0.9 "
"this is the default cd-hit's 'global sequence identity' calculated as: "
"number of identical amino acids in alignment divided by "
"the full length of the shorter sequence",
equate=False),
_Option(['-G', 'global_seq_id'],
"use global sequence identity, default 1 "
"if set to 0, then use local sequence identity, calculated as : "
"number of identical amino acids in alignment "
"divided by the length of the alignment "
"NOTE!!! don't use -G 0 unless you use alignment coverage controls "
"see options -aL (kwarg: `cov_alignment_long`), -AL (kwarg: `cov_alignment_long_control`),"
" -aS (kwarg: `cov_alignment_short`), -AS (kwarg: `cov_alignment_short_control`)",
equate=False),
_Option(['-b', 'band_width'],
'band_width of alignment, default 20',
equate=False),
_Option(['-M', 'memory_limit'],
'memory limit (in MB) for the program, default 800; 0 for unlimited',
equate=False),
_Option(['-T', 'num_threads'],
'number of threads, default 1; with 0, all CPUs will be used',
equate=False),
_Option(['-n', 'word_length'],
"word_length, default 5, see user's guide for choosing it",
equate=False),
_Option(['-l', 'len_throw_away_seqs'],
"length of throw_away_sequences, default 10",
equate=False),
_Option(['-t', 'tol_4_redundance'],
"tolerance for redundance, default 2",
equate=False),
_Option(['-d', 'len_desc'],
"length of description in .clstr file, default 20 "
"if set to 0, it takes the fasta defline and stops at first space "
"-s length difference cutoff, default 0.0",
equate=False),
_Option(['-s', 'len_diff_cutoff'],
"length difference cutoff, default 0.0 "
"if set to 0.9, the shorter sequences need to be "
"at least 90% length of the representative of the cluster",
equate=False),
_Option(['-S', 'len_diff_cutoff_aa'],
"length difference cutoff in amino acid, default 999999 "
"if set to 60, the length difference between the shorter sequences "
"and the representative of the cluster can not be bigger than 60",
equate=False),
_Option(['-aL', 'cov_alignment_long'],
"alignment coverage for the longer sequence, default 0.0 "
"if set to 0.9, the alignment must covers 90% of the sequence",
equate=False),
_Option(['-AL', 'cov_alignment_long_control'],
"alignment coverage control for the longer sequence, default 99999999 "
"if set to 60, and the length of the sequence is 400, "
"then the alignment must be >= 340 (400-60) residues",
equate=False),
_Option(['-aS', 'cov_alignment_short'],
"alignment coverage for the shorter sequence, default 0.0 "
"if set to 0.9, the alignment must covers 90% of the sequence",
equate=False),
_Option(['-AS', 'cov_alignment_short_control'],
"alignment coverage control for the shorter sequence, default 99999999 "
"if set to 60, and the length of the sequence is 400, "
"then the alignment must be >= 340 (400-60) residues",
equate=False),
_Option(['-A', 'cov_alignment'],
"minimal alignment coverage control for the both sequences, default 0 "
"alignment must cover >= this value for both sequences",
equate=False),
_Option(['-uL', 'max_unmatched_percentage_long'],
"maximum unmatched percentage for the longer sequence, default 1.0 "
"if set to 0.1, the unmatched region (excluding leading and tailing gaps) "
"must not be more than 10% of the sequence",
equate=False),
_Option(['-uS', 'max_unmatched_percentage_short'],
"maximum unmatched percentage for the shorter sequence, default 1.0 "
"if set to 0.1, the unmatched region (excluding leading and tailing gaps) "
"must not be more than 10% of the sequence",
equate=False),
_Option(['-U', 'len_max_unmatched'],
"maximum unmatched length, default 99999999 "
"if set to 10, the unmatched region (excluding leading and tailing gaps) "
"must not be more than 10 bases",
equate=False),
_Option(['-B', 'hdd_storage'],
"1 or 0, default 0, by default, sequences are stored in RAM "
"if set to 1, sequence are stored on hard drive "
"it is recommended to use -B 1 for huge databases",
equate=False),
_Option(['-p', 'aln_overlap_2_file'],
"1 or 0, default 0 "
"if set to 1, print alignment overlap in .clstr file",
equate=False),
_Option(['-g', 'accurate_mode'],
"1 or 0, default 0 "
"by cd-hit's default algorithm, a sequence is clustered to the first "
"cluster that meet the threshold (fast cluster). If set to 1, the program "
"will cluster it into the most similar cluster that meet the threshold "
"(accurate but slow mode) "
"but either 1 or 0 won't change the representatives of final clusters",
equate=False),
_Option(['-bak', 'backup'],
"write backup cluster file (1 or 0, default 0)",
equate=False),
]
AbstractCommandline.__init__(self, cmd, **kwargs)
