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"""
Command line object for map_align contact map alignment application
"""
from Bio.Application import _Option
from Bio.Application import AbstractCommandline
[docs]class MapAlignCommandline(AbstractCommandline):
"""
Command line object for map_align [#]_ [#]_
https://github.com/sokrypton/map_align
Examples
--------
>>> from conkit.applications import MapAlignCommandline
>>> mapalign_cline = MapAlignCommandline(map_a='cmap_1.mapalign', map_b='cmap_2.mapalign')
>>> print(mapalign_cline)
map_align cmap_1.mapalign cmap_2.mapalign
You would typically run the command line with :func:`mapalign_cline` or via
the :mod:`~subprocess` module.
"""
def __init__(self, cmd="map_align", **kwargs):
self.parameters = [
_Option(
["-a", "contact_map_a"],
"contact map A",
filename=True,
equate=False,
is_required=True,
),
_Option(
["-b", "contact_map_b"],
"contact map B",
filename=True,
equate=False,
is_required=True,
),
_Option(["-gap_o", "gap_opening_penalty"], "Gap opening penalty [default=-1]", equate=False),
_Option(["-gap_e", "gap_extension_penalty"], "Gap extension penalty [default=-0.01]", equate=False),
_Option(["-sep_cut", "seq_separation_cutoff"], "Sequence separation cutoff [default=3]", equate=False),
_Option(["-iter", "n_iterations"], "Number of iterations [default=20]", equate=False),
]
AbstractCommandline.__init__(self, cmd, **kwargs)
