lib/IMP/multifit/merge_tree.py

#!/usr/bin/env python

from __future__ import print_function
import IMP.multifit
from IMP import ArgumentParser

__doc__ = "Show the DOMINO merge tree to be used in alignment."

def parse_args():
    desc =  """
Show the DOMINO merge tree to be used in the alignment procedure
"""
    p = ArgumentParser(description=desc)
    p.add_argument("assembly_file", help="assembly file name")
    p.add_argument("proteomics_file", help="proteomics file name")
    p.add_argument("mapping_file", help="mapping file name")
    p.add_argument("param_file", help="parameter file name")
    return p.parse_args()


def run(asmb_fn, proteomics_fn, mapping_fn, params_fn):
    asmb = IMP.multifit.read_settings(asmb_fn)
    asmb.set_was_used(True)
    dmap = IMP.em.read_map(asmb.get_assembly_header().get_dens_fn())
    dmap.get_header().set_resolution(
        asmb.get_assembly_header().get_resolution())
    threshold = asmb.get_assembly_header().get_threshold()
    dmap.update_voxel_size(asmb.get_assembly_header().get_spacing())
    dmap.set_origin(asmb.get_assembly_header().get_origin())

    alignment_params = IMP.multifit.AlignmentParams(params_fn)
    alignment_params.show()
    IMP.set_log_level(IMP.WARNING)
    prot_data = IMP.multifit.read_proteomics_data(proteomics_fn)

    mapping_data = IMP.multifit.read_protein_anchors_mapping(prot_data,
                                                             mapping_fn)

    em_anchors = mapping_data.get_anchors()

    # load all proteomics restraints
    align = IMP.multifit.ProteomicsEMAlignmentAtomic(mapping_data, asmb,
                                                     alignment_params)

    align.set_fast_scoring(False)
    align.set_density_map(dmap, threshold)
    align.add_states_and_filters()
    align.add_all_restraints()
    print("\n\n\nDOMINO MERGE TREE\n\n")
    align.show_domino_merge_tree()


def main():
    args = parse_args()
    run(args.assembly_file, args.proteomics_file, args.mapping_file,
        args.param_file)

if __name__ == "__main__":
    main()