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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 :mod:`~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)
