Source code for ample.util.argparse_util

"""
Below is code for creating a boolean argument parser with a default, and a range of choices

class BoolAction(argparse.Action):
    def __call__(self, parser, namespace, values, option_string=None):
        if values is None: values = self.default
        if values in [ '0', 'f', 'F', 'false', 'False', False ]:
            values=False
        elif values in [ '1', 't', 'T', 'true', 'True', True ]:
            values=True
        else:
            msg = 'Unrecognised True/False value: {0}'.format(values)
            raise argparse.ArgumentError(self, msg)
        setattr(namespace, self.dest, values)

parser = argparse.ArgumentParser()

parser.add_argument('-d', '--debug', action=BoolAction, default=True, metavar='True/False', nargs='?', help="debug")
# print(parser.parse_args('-d 2'.split()))
print(parser.parse_args('-d false'.split()))

"""

__author__ = "Jens Thomas & Felix Simkovic"
__date__ = "03 Apr 2016"
__version__ = "1.0"

import argparse

from ample.util import version


[docs]def add_core_options(parser=None):
    """Function to add any arguments required by all runtypes"""
    if parser is None:
        parser = argparse.ArgumentParser()

    parser.add_argument('-config_file', help="user configuration file")

    parser.add_argument('-debug', metavar='True/False',
                        help=argparse.SUPPRESS)

    parser.add_argument('-nproc', type=int,
                        help="Number of processors [1]. For local, serial runs the jobs will be split across nproc processors." +
                        "For cluster submission, this should be the number of processors on a node.")

    parser.add_argument('-work_dir',
                        help='Path to the directory where the job will run (will be created if it doesn\'t exist)')
    return parser


[docs]def add_cluster_submit_options(parser=None):
    """Add the options for submission to a cluster queuing system"""
    if parser is None:
        parser = argparse.ArgumentParser()

    submit_group = parser.add_argument_group(
        'Cluster queue submission options')

    submit_group.add_argument('-submit_array', metavar='True/False',
                              help='Submit SGE jobs as array jobs')

    submit_group.add_argument('-submit_cluster', metavar='True/False',
                              help='Submit jobs to a cluster - need to set -submit_qtype flag to specify the batch queue system.')

    submit_group.add_argument('-submit_max_array', type=int,
                              help='The maximum number of jobs to run concurrently with SGE array job submission')

    submit_group.add_argument('-submit_num_array_jobs', type=int,
                              help='The number of jobs to run concurrently with SGE array job submission')

    submit_group.add_argument('-submit_pe_lsf',
                              help='Cluster submission: string to set number of processors for LSF queueing system')

    submit_group.add_argument('-submit_pe_sge',
                              help='Cluster submission: string to set number of processors for SGE queueing system')

    submit_group.add_argument('-submit_queue',
                              help='The queue to submit to on the cluster.')

    submit_group.add_argument('-submit_qtype',
                              help='Cluster submission queue type - currently support SGE and LSF')
    return parser


[docs]def add_general_options(parser=None):

    if parser is None:
        parser = argparse.ArgumentParser()

    # Always add the core option
    add_core_options(parser)

    parser.add_argument('-alignment_file',
                        help='Alignment file in fasta format. For homologues the first line of each sequence must be the pdb file name')

    parser.add_argument('-allow_his_tag', metavar='True/False',
                        help='Allow HIS tags in the input sequence')

    parser.add_argument('-blast_dir',
                        help='Directory where ncbi blast is installed (binaries in expected in bin subdirectory)')

    parser.add_argument('-classic_mode', metavar='True/False',
                        help='Preset options to run the original AMPLE clustering/truncation options (1 cluster, 3 subclustering radii, 3 sidechains)')

    parser.add_argument('-ccp4i2_xml',
                        help='Path to CCP4I2 XML file - if not None indicates we are running under CCP4I2')

    parser.add_argument('-devel_mode', metavar='devel_mode',
                        help='Preset options to run in development mode - takes longer')

    parser.add_argument('-dry_run', metavar='True/False',
                        help='Check if input files and supplied options are valid.')

    parser.add_argument('-early_terminate', metavar='True/False',
                        help='Stop the run as soon as a success has been found.')

    parser.add_argument('-ensembles',
                        help='Path to directory containing existing ensembles')

    parser.add_argument('-fasta',
                        help='protein fasta file. (required)')

    parser.add_argument('-fast_protein_cluster_exe',
                        help='path to fast_protein_cluster executable')

    parser.add_argument('-F', metavar='flag for F',
                        help='Flag for F column in the MTZ file')

    parser.add_argument('-FREE', metavar='flag for FREE',
                        help='Flag for FREE column in the MTZ file')

    parser.add_argument('-ideal_helices', metavar='True/False',
                        help='Use ideal polyalanine helices to solve structure (8 helices: from 5-40 residues)')

    parser.add_argument('-improve_template', metavar='improve_template',
                        help='Path to a template to improve - NMR, homolog')

    parser.add_argument('-LGA', metavar='path_to_LGA dir',
                        help=argparse.SUPPRESS)  # help='pathway to LGA folder (not the exe) will use the \'lga\' executable. UNUSED')

    parser.add_argument('-make_models', metavar='True/False',
                        help='run rosetta modeling, set to False to import pre-made models (required if making models locally default True)')

    parser.add_argument('-max_array_jobs',
                        help='Maximum number of array jobs to run')

    parser.add_argument('-missing_domain', metavar='True/False',
                        help='Modelling a missing domain - requires domain_all_chains_pdb argument')

    parser.add_argument('-models', metavar='models',
                        help='Path to a folder of PDB decoys, or a tarred and gzipped/bziped, or zipped collection of decoys')

    parser.add_argument('-mr_sequence',
                        help="sequence file for crystal content (if different from what's given by -fasta)")

    parser.add_argument('-mtz', metavar='MTZ in',
                        help='The MTZ file with the reflection data.')

    parser.add_argument('-name', metavar='job_name',
                        help='4-letter identifier for job [ampl]')

    parser.add_argument('-native_pdb', metavar='native_pdb',
                        help='Path to the crystal structure PDB for benchmarking.')

    parser.add_argument('-native_mtz', metavar='native_pdb',
                        help='Path to the native MTZ containing FC and PHIC calculated phases for benchmarking.')

    parser.add_argument('-nmodels', metavar='number of models', type=int,
                        help='number of models to make (default: 1000)')

    parser.add_argument('-nr', metavar='nr',
                        help='Path to the NR non-redundant sequence database')

    parser.add_argument('-nmr_model_in', metavar='nmr_model_in',
                        help='PDB with NMR models')

    parser.add_argument('-nmr_process', type=int,
                        help='number of times to process the NMR models')

    parser.add_argument('-nmr_remodel', metavar='True/False',
                        help='Remodel the NMR structures')

    parser.add_argument('-nmr_remodel_fasta',
                        help='The FASTA sequence to be used for remodelling the NMR ensemble if different from the default FASTA sequence')

    parser.add_argument('-no_gui', metavar='True/False',
                        help='Do not display the AMPLE gui.')

    parser.add_argument('-purge', metavar='True/False',
                        help='Delete all intermediate files and failed MRBUMP results')

    parser.add_argument('-psipred_ss2', metavar='PSIPRED_FILE',
                        help='Psipred secondary structure prediction file')

    parser.add_argument('-quick_mode', metavar='True/False',
                        help='Preset options to run quickly, but less thoroughly')

    parser.add_argument('-restart_pkl', help='Rerun a job using the pickled ample dictionary')

    parser.add_argument('-run_dir', metavar='run_directory',
                        help='Directory where the AMPLE work directory will be created [current dir]')
    
    parser.add_argument('-rvapi_document',
                        help='Path to an existing rvapi document (for running under jscofe)')

    parser.add_argument('-scwrl_exe', metavar='path to scwrl',
                        help='Path to Scwrl4 executable')

    parser.add_argument('-single_model',
                        help='Single structure model to be used to create ensembles')

    parser.add_argument('-sf_cif',
                        help='Path to a structure factor CIF file (instead of MTZ file)')

    parser.add_argument('-SIGF',
                        help='Flag for SIGF column in the MTZ file')

    parser.add_argument('-spicker_exe',
                        help='Path to spicker executable')

    parser.add_argument('-top_model_only', metavar='True/False',
                        help='Only process the top model in each ensemble')

    parser.add_argument('--version', action='version',
                        version='%(prog)s {0}'.format(version.__version__))

    parser.add_argument('-webserver_uri',
                        help='URI of the webserver directory - also indicates we are running as a webserver')
    return parser


[docs]def add_contact_options(parser=None):
    """Contact prediction related options"""
    if parser is None:
        parser = argparse.ArgumentParser()

    contact_group = parser.add_argument_group("Contact Restraints Options")

    contact_group.add_argument('-bbcontacts_file',
                               help='Additional bbcontacts file. Requires normal contactfile')

    contact_group.add_argument('-bbcontacts_format',
                               help='Residue contact file format. For available formats refer to the AMPLE documentation')

    contact_group.add_argument('-contact_file',
                               help='Residue contact file')

    contact_group.add_argument('-contact_format',
                               help='Residue contact file format. For available formats refer to the AMPLE documentation')

    contact_group.add_argument('-disulfide_constraints_file',
                               help='Disulfide residue constraints for ab initio modelling')

    contact_group.add_argument('-distance_to_neighbour', type=int,
                               help="Min. distance between residue pairs for contact (default=5)")

    contact_group.add_argument('-energy_function',
                               help='Rosetta energy function for contact restraint conversion (default=FADE)')

    contact_group.add_argument('-native_cutoff', type=float,
                               help='Distance cutoff for reference contacts in native structure (default=8A)')

    contact_group.add_argument('--no-contact-prediction', default=False, action="store_true",
                               help="Do not predict contacts")

    contact_group.add_argument('-restraints_factor', type=float,
                               help='Factor (* Sequence length) determining number of contact restraints to use (default=1.0)')

    contact_group.add_argument('-restraints_file',
                               help='Residue restraints for ab initio modelling')

    contact_group.add_argument('-restraints_weight', type=float,
                               help="Additional energy weighting of restraints in Rosetta")

    contact_group.add_argument('-subselect_mode',
                               help="Long-range decoy satisfaction subselection mode - one of [{0}]".format(" | ".join(["linear", "scaled", "cutoff"])))

    return parser


[docs]def add_mr_options(parser=None):

    if parser is None:
        parser = argparse.ArgumentParser()

    mr_group = parser.add_argument_group(
        'MRBUMP/Molecular Replacement Options')

    mr_group.add_argument('-arpwarp_cycles', type=int,
                          help='The number of ArpWarp cycles to run')

    mr_group.add_argument('-buccaneer_cycles', type=int,
                          help='The number of Bucanner rebuilding cycles to run')

    mr_group.add_argument('-do_mr', metavar='True/False',
                          help='Run or skip the Molecular Replacement step')

    mr_group.add_argument('-domain_all_chains_pdb',
                          help='Fixed input to mr bump')

    mr_group.add_argument('-domain_termini_distance',
                          help='distance between termini for insert domains')

    mr_group.add_argument('-molrep_only', metavar='True/False',
                          help='Only use Molrep for Molecular Replacement step in MRBUMP')

    mr_group.add_argument('-mrbump_dir',
                          help='Path to a directory of MRBUMP jobs (see restart_pkl)')

    mr_group.add_argument('-mr_keys', nargs='+', action='append',
                          help='Additional keywords for MRBUMP - are passed through without editing')

    mr_group.add_argument('-mr_sg_all', metavar='True/False',
                          help='Try all possible space groups in PHASER Molecular Replacement step in MRBUMP')

    mr_group.add_argument('-nmasu', type=int,
                          help='Manually specify the number of molecules in the asymmetric unit - sets the NMASu MRBUMP flag')

    mr_group.add_argument('-phaser_kill', metavar='phaser_kill', type=int,
                          help='Time in minutes after which phaser will be killed (0 to leave running)')

    mr_group.add_argument('-phaser_only', metavar='True/False',
                          help='Only use Phaser for Molecular Replacement step in MRBUMP')

    mr_group.add_argument('-phaser_rms', metavar='phaser_rms',
                          help='RMS value for phaser')

    mr_group.add_argument('-refine_rebuild_arpwarp', metavar='True/False',
                          help='True to use ARPWARP to rebuild the REFMAC-refined MR result.')

    mr_group.add_argument('-refine_rebuild_buccaneer', metavar='True/False',
                          help='True to use Buccaneer to rebuild the REFMAC-refined MR result.')
    
    mr_group.add_argument('-shelx_cycles',
                          help='The number of shelx cycles to run when rebuilding.')

    mr_group.add_argument('-shelxe_exe', metavar='path to shelxe executable',
                          help='Path to the shelxe executable')

    mr_group.add_argument('-shelxe_rebuild', metavar='True/False',
                          help='Rebuild shelxe traced pdb with buccaneer and arpwarp')

    mr_group.add_argument('-shelxe_rebuild_arpwarp', metavar='True/False',
                          help='Rebuild shelxe traced pdb with arpwarp')

    mr_group.add_argument('-shelxe_rebuild_buccaneer', metavar='True/False',
                          help='Rebuild shelxe traced pdb with buccaneer')


    mr_group.add_argument('-use_scwrl', metavar='True/False',
                          help='Remodel sidechains of the decoy models using Scwrl4')

    mr_group.add_argument('-use_shelxe', metavar='True/False',
                          help='True to use shelxe')
    return parser


[docs]def add_rosetta_options(parser=None):

    if parser is None:
        parser = argparse.ArgumentParser()

    rosetta_group = parser.add_argument_group('ROSETTA Modelling Options')

    rosetta_group.add_argument('-all_atom', metavar='True/False',
                               help="Do all-atom Rosetta modelling (adds \"-return_full_atom true\" to rosetta arguments")

    rosetta_group.add_argument('-frags_3mers',
                               help='Path to file with pre-existing Rosetta 3mer fragments')

    rosetta_group.add_argument('-frags_9mers',
                               help='Path to file with pre-existing Rosetta 3mer fragments')

    rosetta_group.add_argument('-make_frags', metavar='True/False',
                               help='set True to generate Rosetta 3mers and 9mers locally, False to import fragments')

    rosetta_group.add_argument('-rg_reweight', metavar='radius of gyration reweight', type=float,
                               help='Set the Rosetta -rg_reweight flag to specify the radius of gyration reweight.')

    rosetta_group.add_argument('-rosetta_AbinitioRelax',
                               help='Path to Rosetta AbinitioRelax executable')

    rosetta_group.add_argument('-ROSETTA_cluster',
                               help='location of rosetta cluster')

    rosetta_group.add_argument('-rosetta_db',
                               help='Path to the Rosetta database directory')

    rosetta_group.add_argument('-rosetta_dir',
                               help='The Rosetta install directory')

    rosetta_group.add_argument('-rosetta_fragments_exe',
                               help='Location of the Rosetta make_fragments.pl script')

    rosetta_group.add_argument('-rosetta_version', type=float,
                               help='The version number of Rosetta')

    rosetta_group.add_argument('-transmembrane', metavar='True/False',
                               help='Do Rosetta modelling for transmembrane proteins (Ovchinnikov protocol)')

    rosetta_group.add_argument('-transmembrane_old', metavar='True/False',
                               help='Do Rosetta modelling for transmembrane proteins (Yarov-Yarovoy protocol)')

    rosetta_group.add_argument('-transmembrane_octopusfile',
                               help='Octopus transmembrane topology predicition file')

    rosetta_group.add_argument('-transmembrane_spanfile',
                               help='Span file for modelling transmembrane proteins')

    rosetta_group.add_argument('-transmembrane_lipofile',
                               help='Lips4 file for modelling transmembrane proteins')

    rosetta_group.add_argument('-use_homs', metavar='True/False',
                               help="Select ROSETTA fragments from homologous models")
    return parser