Initial commit

.gitignore

+# Created by .ignore support plugin (hsz.mobi)
+.venv
+data/examples
+.idea
\ No newline at end of file

MANIFEST.in

+graft ariaec/conf
+graft ariaec/templates
+graft ariaec/data
\ No newline at end of file

ariaec/__init__.py

+
+

ariaec/base.py

+"""
+                            Basic tools aria_ec
+"""
+from __future__ import absolute_import, division, print_function
+
+import logging
+import logging.config
+import os
+import json
+import re
+import ast
+import sys
+import numpy as np
+import pkg_resources as pkgr
+import matplotlib.artist as art
+from cStringIO import StringIO
+
+
+logger = logging.getLogger()
+
+
+def titleprint(outfile, progname='', desc=''):
+    """
+    Init log file
+    :param outfile:
+    :param progname: docstring
+    :param desc:
+    :return:
+    """
+    out = '''
+================================================================================
+{progname}
+                                {desc}
+================================================================================
+'''.format(progname=progname, desc=desc.capitalize())
+    outfile.write(out[1:])
+
+
+def get_filename(path):
+    """
+    Search filename in the given path
+    :param path:
+    :return:
+    """
+    return "_".join(path.split("/")[-1].split(".")[:-1])
+
+
+def reg_load(regex, filepath, sort=None):
+    """
+
+    :param regex:
+    :param filepath:
+    :param sort:
+    :return:
+    """
+
+    lines_dict = {}
+
+    with open(filepath) as f:
+        for index, line in enumerate(f):
+            match = regex.match(line)
+            if match:
+                lines_dict[index] = match.groupdict()
+
+    if sort:
+        lines_dict = sort_2dict(lines_dict, sort)
+
+    return lines_dict
+
+
+def sort_2dict(unsort_dict, key, reverse=True):
+    """
+    Sort 2d dict by key
+    :param reverse:
+    :param key:
+    :param unsort_dict:
+    :return: sorted dict
+    """
+    sorted_index = sorted(unsort_dict, key=lambda x: float(unsort_dict[x][key]),
+                          reverse=reverse)
+    sorted_dict = {}
+
+    for rank, ind in enumerate(sorted_index):
+        sorted_dict[rank + 1] = unsort_dict[ind]
+
+    return sorted_dict
+
+
+def cart_dist(x, y):
+    """
+    Evaluate cartesian distance beetween 2 points x, y
+    :param x: numpy array (len = n dimensions)
+    :param y: numpy array (len = n dimensions)
+    :return:
+    """
+    return np.sqrt(sum(np.power(x - y, 2)))
+
+
+def format_str(string):
+    """
+    Convert str in bool, float, int or str
+    :param string:
+    :return:
+    """
+    if re.search("^\s*true\s*$", string, re.I):
+        return True
+    elif re.search("^\s*false\s*$", string, re.I):
+        return False
+    elif re.search("^\s*\d+\s*$", string):
+        return int(string)
+    elif re.search("^[\s\d-]+\.\d+\s*$", string):
+        return float(string)
+    elif "," in string:
+        return string.split(',')
+    elif "+" in string:
+        return string.split('+')
+    elif re.search("[/\\w]+", string):
+        return string
+    else:
+        if string:
+            try:
+                ev_str = ast.literal_eval(string)
+            except ValueError:
+                logger.error("Don't understand given string %s. Please check "
+                             "format." % string)
+                return None
+            except SyntaxError:
+                logger.error("Given string %s is not a valid expression" % string)
+                return None
+            return ev_str
+        else:
+            return None
+
+
+def format_dict(indict):
+    for key in indict:
+        indict[key] = format_str(indict[key])
+    return indict
+
+
+def ppdict(indict, indent=2):
+    return json.dumps(indict, indent=indent)
+
+
+def tickmin(pandata, ntick=None, shift=0, offset=5):
+    """
+    Minimise number of ticks labels for matplotlib or seaborn plot
+    :param offset:
+    :param shift:
+    :param pandata: pandas dataframe
+    :param ntick: number of ticks wanted per axes
+    :return:
+    """
+    yticks = [_ + shift for _ in range(0, len(pandata.index))]
+    xticks = [_ + shift for _ in range(0, len(pandata.columns))]
+    if ntick:
+        keptticks = yticks[::(len(pandata.index) // int(ntick))]
+        yticks = [_ if _ in keptticks else '' for _ in yticks]
+        # If shift != 0, need to initialize first value of ticks
+
+        keptticks = xticks[::(len(xticks) // int(ntick))]
+        xticks = [_ if _ in keptticks else '' for _ in xticks]
+    else:
+        keptticks = [ytick for i, ytick in enumerate(yticks)
+                     if (i + shift) % offset == 0]
+        # keptticks = yticks[::offset - shift]
+        yticks = [_ if _ in keptticks else '' for _ in yticks]
+        # If shift != 0, need to initialize first value of ticks
+
+        keptticks = [xtick for i, xtick in enumerate(xticks)
+                     if (i + shift) % offset == 0]
+        # keptticks = xticks[::offset - shift]
+        xticks = [_ if _ in keptticks else '' for _ in xticks]
+    return xticks, yticks
+
+
+def tickrot(axes, figure, rotype='horizontal', x=True, y=True):
+    """
+    Matplot rotation of ticks labels
+    :param axes:
+    :param figure:
+    :param rotype:
+    :param x:
+    :param y:
+    :return:
+    """
+    if y:
+        art.setp(axes.get_yticklabels(), rotation=rotype)
+    if x:
+        art.setp(axes.get_xticklabels(), rotation=rotype)
+    figure.canvas.draw()
+
+
+class CustomLogging:
+    # default_file = os.path.join(os.path.abspath(os.path.dirname(__file__)),
+    #                             "conf/logging.json")
+    default_file = "conf/logging.json"
+
+    def __init__(self, level=logging.INFO, desc=None):
+        # TODO: detect path log filenames and makedirs if not exists
+        logging.basicConfig(level=level)
+        if desc:
+            self.msg = desc.strip()
+        else:
+            self.msg = ""
+        self.config = self.default_config()
+
+    def update_msg(self, desc):
+        if type(self.msg) == list:
+            self.msg += desc
+            self.msg = " - ".join(self.msg)
+        elif type(self.msg) == str:
+            self.msg = " - ".join((self.msg, desc.capitalize()))
+
+    def default_config(self):
+        # with open(self.default_file, 'rt') as f:
+        with pkgr.resource_stream(__name__, self.default_file) as f:
+            config = json.load(f)
+            logging.config.dictConfig(config)
+        return config
+
+    def set_outdir(self, outdir):
+        """
+        Create log directory and change log files location
+        :param outdir: path output directory
+        :return:
+        """
+        outdir = os.path.join(outdir, "log") if "log" not in outdir else outdir
+        if not os.path.exists(os.path.abspath(outdir)):
+            os.makedirs(outdir)
+        if outdir and "handlers" in self.config:
+            for hand in self.config["handlers"]:
+                if "filename" in self.config["handlers"][hand]:
+                    self.config["handlers"][hand]["filename"] = \
+                        os.path.join(outdir, os.path.basename(
+                            self.config["handlers"][hand]["filename"]))
+            logging.config.dictConfig(self.config)
+
+    def welcome(self):
+        desc = '''
+================================================================================
+
+{:^80}
+
+================================================================================
+'''.format(self.msg)
+        print(desc)
+
+
+class Capturing(list):
+    def __enter__(self):
+        # Stock default stdout and redirect current stdout to this class
+        self._stdout = sys.stdout
+        # All print calls are saved into self._stringio
+        sys.stdout = self._stringio = StringIO()
+        return self
+
+    def __exit__(self, *args):
+        self.extend("\n".join(self._stringio.getvalue().splitlines()))
+        sys.stdout = self._stdout
+
+
+if __name__ == "__main__":
+    # Test Logger
+    CustomLogging().set_outdir("../examples/out")
+    logger = logging.getLogger("TEST")
+    print(dir(logger))
+    logger.info("Log test")

ariaec/commands.py

+"""
+                            Input/Output aria_ec
+"""
+from __future__ import absolute_import, division, print_function
+
+import os
+import logging
+import argparse as argp
+
+from .ecsettings import AriaEcSettings
+from .maplot import AriaEcContactMap
+from .econverter import AriaEcBbConverter
+from .setup import AriaEcSetup
+
+logger = logging.getLogger(__name__)
+
+
+def check_file(prospective_file):
+
+    if not os.path.exists(prospective_file):
+        raise argp.ArgumentTypeError("readable_file:'{0}' is not a valid "
+                                     "path".format(prospective_file))
+    if not os.access(prospective_file, os.R_OK):
+        raise argp.ArgumentTypeError("readable_file:'{0}' is not a readable "
+                                     "file".format(prospective_file))
+
+
+class ReadableFile(argp.Action):
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        if type(values) == list:
+            for prospective_file in values:
+                check_file(prospective_file)
+        elif type(values) == str:
+            check_file(values)
+        setattr(namespace, self.dest, values)
+
+
+# TODO: Make parent Command class with _create_argparser, self.args,
+# update_logger and run
+class AriaEcCommand:
+    """
+    Argparse interface for aria_ec
+    """
+
+    command_list = ("setup", "bbconv", "contactmap")
+    desc_list = (u"Setup ARIA infrastructure with given contacts translated "
+                 u"into ARIA restraints",
+                 u"Convert contacts in bbcontact format",
+                 u"Contactmap tool")
+    contact_types = ("plmdca", "evfold", "bbcontacts", "pconsc", "gremlin",
+                     "metapsicov", "pdb", "native", "native_full",
+                     "contactlist")
+    default_confile = "conf/aria_ec.ini"
+
+    def __init__(self, custom_logging=None):
+        # Def Argument parser
+        parser = self._create_argparser()
+        # parse args
+        self.args = parser.parse_args()
+        # Update logger with outdir
+        self._update_logger(custom_logging)
+
+    def _update_logger(self, log):
+        if log and hasattr(self.args, "output_directory"):
+            log.set_outdir(self.args.output_directory)
+            log.update_msg(self.args.command)
+            log.welcome()
+
+    def _create_argparser(self):
+        parser = argp.ArgumentParser(description=u"ARIA Evolutionary "
+                                                 u"restraints toolbox",
+                                     formatter_class=argp.ArgumentDefaultsHelpFormatter)
+        parser.add_argument("-o", "--output", dest="output_directory",
+                            type=str, help="Output directory")
+        parser.add_argument("-c", "--conf", action=ReadableFile, dest="conf_file",
+                            default=None, help="configuration file")
+        # Create subcommands
+        self._create_subparsers(parser.add_subparsers(dest="command"))
+        return parser
+
+    def _create_subparsers(self, parser):
+        """
+        Generate subcommands
+        :param parser: argparser object
+        :return:
+        """
+        for index, command in enumerate(self.command_list):
+            # Create subparser defined in command list
+            subcommand = getattr(self, "_" + command + "_parser")(desc=self.desc_list[
+                index])
+            parser.add_parser(command, parents=[subcommand])
+
+    def _setup_parser(self, desc=None):
+        """
+        setup opt & args
+        :param desc: command descriptor
+        :return: argparser object
+        """
+        parser = argp.ArgumentParser(description=desc,
+                                     add_help=False)
+        # Options
+        # Args
+        group = parser.add_argument_group('required arguments')
+        group.add_argument("seq", action=ReadableFile,
+                           help="sequence file [FASTA]")
+        group.add_argument("sspred", action=ReadableFile,
+                           help="secondary structure prediction file")
+        group.add_argument("infiles", nargs="+", metavar="infile",
+                           action=ReadableFile,
+                           help="contact or pdb file(s) used to build aria "
+                                "distance restraints")
+        group.add_argument("-d", "--distfile", dest="distfile",
+                           help="Pdb or distance matrix iif distance_type "
+                                "set  to   distfile in conf  file,  "
+                                "use distances in the  given file as "
+                                "target  distance to build  distance "
+                                "restraints")
+        group.add_argument("-t", "--type", required=True,
+                           nargs="+", dest="contact_types",
+                           choices=self.contact_types, help="Infile(s) contact "
+                                                            "type(s)")
+        group.add_argument("-r", "--ref", dest="ref",
+                           help="Native pdb. Allow TP/FP detection.")
+        group.add_argument("--hb", dest="hb",
+                           help="H-bonds contact file (eg: metapsicov.hb)")
+        group.add_argument("--ssidx", dest="ssidx", action="store_true",
+                           default=False, help="Use secondary structure index")
+        return parser
+
+    def _bbconv_parser(self, desc=None):
+        """
+        bbconv opt & args
+        :param desc: command descriptor
+        :return: argparser object
+        """
+        parser = argp.ArgumentParser(description=desc,
+                                     add_help=False)
+        # args
+        parser.add_argument("contactfile", help="contacts file (pconsc, plm)",
+                            action=ReadableFile)
+        parser.add_argument("sspred", help="psipred file",
+                            action=ReadableFile)
+        parser.add_argument("seq", help="sequence file [FASTA]",
+                            action=ReadableFile)
+        parser.add_argument("msa", nargs='?',
+                            help="MSA [FASTA] for diversityvalue"
+                                 "used with bbcontacts")
+        parser.add_argument("-t", "--type", required=True, dest="contact_type",
+                            choices=self.contact_types, help="Infile contact "
+                                                             "type")
+        return parser
+
+    def _contactmap_parser(self, desc=None):
+        """
+        contactmap opt & args
+        :param desc: command descriptor
+        :return: argparser object
+        """
+        parser = argp.ArgumentParser(description=desc,
+                                     add_help=False)
+        parser.add_argument("seq", action=ReadableFile,
+                            help="sequence file [FASTA]")
+        parser.add_argument("sspred", action=ReadableFile,
+                            help="secondary structure prediction file")
+        parser.add_argument("infiles", nargs="+", metavar="infile",
+                            action=ReadableFile,
+                            help="contact or pdb file(s) used to build aria "
+                                 "distance restraints")
+        parser.add_argument("-t", "--type", required=True,
+                            nargs="+", dest="contact_types",
+                            choices=self.contact_types, help="Infile(s) "
+                                                             "contact "
+                                                             "type(s)")
+        parser.add_argument("--nofilter", dest="nofilter", action="store_true",
+                            default=None, help="Do not use contact list "
+                                               "filter and select top n "
+                                               "contacts")
+        parser.add_argument("--ssidx", dest="ssidx", action="store_true",
+                            default=False,
+                            help="Use secondary structure index")
+        return parser
+
+    def create_settings(self):
+        logger.debug("Create AriaEcSettings")
+        settings = AriaEcSettings()
+        logger.info("Loading default config file")
+        settings.load_config(self.default_confile, pkg=True)
+        if self.args.conf_file:
+            print(self.args.conf_file)
+            logger.info("Updating settings with conf file")
+            settings.load_config(self.args.conf_file)
+        # Update settings associated to command section
+        logger.info("Updating %s settings with args" % self.args.command)
+        getattr(settings, self.args.command).args.update(self.args.__dict__)
+        if self.args.output_directory:
+            logger.info("Updating output directory")
+            settings.infra = self.args.output_directory
+        return settings
+
+    def run(self):
+        # call method relative to args.command
+        logger.info("Run %s command" % self.args.command)
+        getattr(self, self.args.command)()
+
+    def setup(self):
+        setup_inst = AriaEcSetup(self.create_settings())
+        setup_inst.run()
+        # instantiate AriaEcSetup with AriaEcSettings
+
+    def bbconv(self):
+        bbconverter = AriaEcBbConverter(self.create_settings())
+        bbconverter.run()
+
+    def contactmap(self):
+        # instantiate AriaEcContactmap with AriaSettings
+        econtactmap = AriaEcContactMap(self.create_settings())
+        econtactmap.run()
+
+
+if __name__ == "__main__":
+    # Test AriaEcCommand object
+    logging.basicConfig(level=logging.DEBUG)
+    logger = logging.getLogger("IO")
+    argparser = AriaEcCommand()

ariaec/conf/aria_ec.ini

+[main]
+; ------------------------- Main parameters ---------------------------------- #
+; Leave these fields empty in order to use default files
+ss_dist_file:
+scsc_min_file:
+ariaproject_template:
+
+[contactdef]
+; Contact definition section used to define contactmap from pdb file
+default_cutoff:                             8.0
+ca_ca:
+cb_cb:
+sc_sc:
+; Add other contact cutoff below folowwing the syntax atm1_atm2
+
+[setup]
+; ------------------------------ TBL parameters ------------------------------ #
+; longrange_hb                  : True, False [False]; use long range hbond
+;                                 restraints. If there is no hbond map given,
+;                                 use the naive method from METAPSICOV (Take
+;                                 the top nf_longrange_hb * seq length
+;                                 predicted contacts from the contactlist and
+;                                 set those who are in a beta sheet as hb
+; nf_longrange_hb               : N hbond generated = nf * seq length
+; longrange_hbtype              : main, all; Consider short range hbond only
+;                                 as main chain hydrogen bond or for all
+;                                 donor/acceptor
+; hb_dminus/dplus               : distance bounds in tbl restraints
+longrange_hb:                               False
+nf_longrange_hb:                            0.1
+longrange_hbtype:                           main
+hb_dminus:                                  0.0
+hb_dplus:                                   0.5
+; --------------------------- Contacts parameters ---------------------------- #
+; evfold_weight                 : use EVFold weight -> 10/i (i:contact rank)
+; neighborhood_contact          : add neighbors when writing restraint
+; pair_list                     : all, min [min]; use all atom pairs or
+;                                 minimized list (CA-CA, CB-CB, SC-SC)
+; ambiguous_distance_restraint  : use Ambiguous Distance Restraints
+; ambiguous_distance_type       : min, deff [min]; compute Deff from target
+;                                 distance iif ADR
+; distance_type                 : fixed, pdbstat, distfile [fixed]; fixed use
+;                                 ca, cb and sc upper_bound
+evfold_weight:                              False
+neighborhood_contact:                       False
+pair_list:                                  min
+ambiguous_distance_restraint:               False
+ambiguous_distance_type:                    min
+deffpow:                                    6
+; TODO: move groupby_method to contactdef section
+groupby_method:                             min
+distance_type:                              fixed
+; TODO: move parameters below to contactdef section
+; Parameters below used only when distance_type is set to "fixed"
+restraint_distance:                         2.5
+lower_bound:                                1.0
+def_upper_bound:                            4.0
+ca_upper_bound:                             7.0
+cb_upper_bound:                             7.0
+; ---------------------------- Filter parameters ----------------------------- #
+; n_factor      : Number of EC selected: n * n_factor (n: sequence length)
+; contactfilter : all or combinaison of pos, cons, cys, ssclash, nd
+;                 separated by "+" character [all]
+n_factor:                                   1.0
+contactfilter:
+conservation_treshold:                      95
+position_treshold:                          5
+nd_beta:                                    0.99
+nd_alpha:                                   1.0
+nd_control:                                 0
+; --------------------------- ARIA XML parameters ---------------------------- #
+runid:                                      1
+cpus:                                       100
+host_command:                               sbatch --cores-per-socket=10 -o /baycells/home/fallain/slurm.errors
+working_directory:                          data/examples/out/aria_wd
+temp_root:                                  data/examples/out/aria_tmp
+parameter_definition:                       automatic
+ss_dist_format:                             tbl
+ss_dist_enabled:                            yes
+ss_dist_add_to_network:                     no
+ss_dist_calibrate:                          no
+ss_dist_run_network_anchoring:              no
+ss_dist_filter_contributions:               no
+dist_format:                                xml
+dist_enabled:                               yes
+dist_add_to_network:                        no
+dist_calibrate:                             no
+dist_run_network_anchoring:                 no
+dist_filter_contributions:                  yes
+cns_executable:                             /Bis/home/bardiaux/bin/cns1.21.exe
+cns_keep_output:                            no
+unambiguous_restraints_k_cool1_initial:     10.0
+unambiguous_restraints_k_cool1_final:       50.0
+unambiguous_restraints_k_cool2:             50.0
+hbond_restraints_k_cool1_initial:           10.0
+hbond_restraints_k_cool1_final:             50.0