python-cogent 1.9-9 / usr / lib / python2.7 / dist-packages / cogent / motif / util.py

#!/usr/bin/env python
"""Utility classes for general motif and module API."""

from __future__ import division
from cogent.core.alignment import Alignment
from cogent.core.location import Span

__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Jeremy Widmann", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
__status__ = "Prototype"

class Location(Span):
    """Object that stores location information for a module

    -Sequence refers to the original sequence the module came from
    -SeqId is the key of the sequence in the alignment
    -Start is the position in the sequence

    """

    def __init__(self, SeqId, Start, End=None):
        """Initializes location object"""
        self.SeqId = SeqId
        Span.__init__(self,Start, End)

    def __cmp__(self,other):
        """Overwriting __cmp__ for sorting purposes"""
        return cmp(self.SeqId, other.SeqId)

class ModuleInstanceI(object):
    """Object that stores individual module instance information.

    Contains sequence, location, Pvalue and Evalue of a module instance as well
    as some basic instance functions.
    """

    def __init__(self, Sequence, Location, Pvalue=None, Evalue=None):
        """Initializes ModuleInstance object"""
        self.Sequence = Sequence
        self.Location = Location    #Location Object
        self.Pvalue = Pvalue
        self.Evalue = Evalue

    def distance(self,other):
        """Calculates the distance between two ModuleInstances"""
        raise NotImplementedError

    def __cmp__(self,other):
        """Overwriting __cmp__ function to compare ModuleInstance objects"""
        if self is other:
            return 0
        return cmp(self.Pvalue,other.Pvalue) \
               or cmp(self.Evalue,other.Evalue) \
               or cmp(self.Location,other.Location) \
               or cmp(str(self),str(other))
    
    def __lt__(self, other):
        return cmp(self, other) == -1
    
    def __le__(self, other):
        return cmp(self, other) <= 0

    def __gt__(self, other):
        return cmp(self, other) == 1

    def __ge__(self, other):
        return cmp(self, other) >= 0

    def __eq__(self, other):
        return self.__cmp__(other) == 0
    
    def __ne__(self, other):
        return cmp(self, other) != 0
    
class ModuleInstanceStr(ModuleInstanceI, str):
    """Constructor for ModuleInstance inheriting from string."""
    def __new__(cls, data='', *args, **kwargs):
        return str.__new__(cls, data)
    def __init__(self, *args, **kwargs):
        return ModuleInstanceI.__init__(self, *args, **kwargs)

def ModuleInstance(data, Location, Pvalue=None, Evalue=None, constructor=None):
    """Creates ModuleInstance given a constructor."""
    if constructor is None:
        #maybe add code to try to figure out what to do from the data later
        constructor=ModuleInstanceStr
    return constructor(data, Location, Pvalue, Evalue)

def seqs_from_empty(obj, *args, **kwargs):
    """Allows empty initialization of Module, useful when data must be added."""
    return [], []
    
class Module(Alignment):
    """Object that stores module information.

    Module is an Alignment of ModuleInstances.  Constructed as a dict keyed by
    location with ModuleInstance sequence as the value:
        - {(SeqId, Start): ModuleInstance}
    """
    InputHandlers = Alignment.InputHandlers.copy()
    InputHandlers['empty'] = seqs_from_empty

    def __init__(self, data=None, Template=None, MolType=None,\
                 Locations=None, Pvalue=None, Evalue=None, Llr=None,\
                 ID=None,ConsensusSequence=None):
        """Initializes Module object"""
        self.Template = Template
        if MolType is not None:
            self.MolType = MolType
        self.Pvalue = Pvalue
        self.Evalue = Evalue
        self.Llr = Llr      #Log likelihood ratio
        self.ID = ID
        self.ConsensusSequence = ConsensusSequence
        if isinstance(data, dict):
            data = sorted(data.items())
        else:
            try:
                data = sorted(data)
            except TypeError:
                pass
        super(Module, self).__init__(data, MolType=MolType)

    def update(self, other):
        """Updates self with info in other, in-place. WARNING: No validation!"""
        self.Names += other.Names
        self.NamedSeqs.update(other.NamedSeqs)

    def __setitem__(self, item, val):
        """Replaces item in self.NamedSeqs. WARNING: No validation!"""
        if item not in self.NamedSeqs:
            self.Names.append(item)
        self.NamedSeqs[item] = val

    def __repr__(self):
        return str(self.NamedSeqs)


    def __str__(self):
        """Returns string representation of IUPAC consensus sequence"""
        if len(self.MolType.Alphabet) < 20:
            return str(self.IUPACConsensus(self.MolType))
        return str(''.join(self.majorityConsensus()))

    
    def distance(self,other):
        """Calculates the distance between two Modules"""
        raise NotImplementedError

    def __cmp__(self,other):
        """Overwriting __cmp__ function to compare Module objects"""
        return cmp(self.Pvalue,other.Pvalue) \
               or cmp(self.Evalue,other.Evalue)

    def __hash__(self):
        """overwriting __hash__ function to hash Module object"""
        return id(self)

    def _get_location_dict(self):
        """Returns a dict of module locations.

        Represented as a dict with SeqId as key and [indices] as values:
            {SeqId:[indices]}
        """
        location_dict = {}
        for key in self.Names:
            try:
                location_dict[key[0]].append(key[1])
            except:
                location_dict[key[0]]=[key[1]]
        return location_dict

    LocationDict = property(_get_location_dict)
    
    def _get_loose(self):
        """Returns a list of all ModuleInstances not in self.Strict.
        """
        loose_list = []
        strict = self.Strict[0].Sequence
        for instance in self.values():
            if instance.Sequence != strict:
                loose_list.append(instance)
        return loose_list
        
    Loose = property(_get_loose)
    
    def _get_strict(self):
        """Returns a list of ModuleInstances with the most common sequence.
        """
        strict_dict = {} #Dictionary to hold counts of instance strings.
        #For each ModuleInstance in self.

        for instance in self.values():

            #If instance already in strict_dict then increment and append.
            if instance.Sequence in strict_dict:
                strict_dict[instance.Sequence][0]+=1
                strict_dict[instance.Sequence][1].append(instance)
            #Else, add count and instance to dict.
            else:
                strict_dict[instance.Sequence]=[1,[instance]]
        
        #List with all counts and instances
        count_list = strict_dict.values()
        count_list.sort()
        count_list.reverse()
        #Set self.Template as the Strict ModuleInstance sequence.
        self.Template = count_list[0][1][0].Sequence
        #Return list of ModuleInstances with the most common sequence.
        return count_list[0][1]
    
    Strict = property(_get_strict)
    
    def basePossibilityCount(self,degenerate_dict=None):
        """Returns number of possible combinations to form a degenerate string.
        """
        if degenerate_dict is None:
            degenerate_dict = self.MolType.Degenerates
        #Get degenerate string representation of module
        degenerate_string = self.__str__()
        #Get length of first degenerate character
        combinations = len(degenerate_dict.get(degenerate_string[0],'-'))
        #Multiply number of possibilities for each degenerate character together
        for i in range(1, len(degenerate_string)):
            combinations *= len(degenerate_dict.get(degenerate_string[i],'-'))
        #Return total possible ways to make module
        return combinations

    def _coerce_seqs(self, seqs, is_array):
        """Override _coerce_seqs so we keep the orig objects."""
        return seqs

    def _seq_to_aligned(self, seq, key):
        """Override _seq_to_aligned so we keep the orig objects."""
        return seq

class ModuleFinder(object):
    """Object that constructs a dict of modules given an alignment"""

    def __call__(self, *args):
        """Call method for ModuleFinder"""
        raise NotImplementedError

class ModuleConsolidator(object):
    """Object that takes in a list of modules and returns a consolidated list.
    Modules that are very similar are considered the same module.
    """

    def __call__(self, *args):
        """Call method for ModuleConsolidator"""
        raise NotImplementedError

class Motif(object):
    """Object that stores modules that are considered the same motif
    """

    def __init__(self, Modules=None, Info=None):
        """Initializes Motif object"""
        self.Modules = []
        try:
            #only one module in motif
            self.Modules.append(Modules)
        except:
            #list of modules
            self.Modules.extend(Modules)
        self.Info = Info

class MotifFinder(object):
    """Object that takes modules and constructs motifs

        - Takes in a list of modules and constructs a list of Motifs"""

    def __call__(self, *args):
        """Call method for MotifFinder"""
        raise NotImplementedError

class MotifFormatter(object):
    """Object that takes a list of Motifs and formats them for output to browser

        - Takes in a list of motifs and generates specified output format.
    """
    COLORS = [ "#00FF00","#0000FF", "#FFFF00", "#00FFFF", "#FF00FF",
               "#FAEBD7", "#8A2BE2", "#A52A2A", "#00CC00", "#FF6600",
               "#FF33CC", "#CC33CC", "#9933FF", "#FFCCCC", "#00CCCC", 
               "#CC6666", "#CCCC33", "#66CCFF", "#6633CC", "#FF6633" ]

    STYLES = ["", "font-weight: bold", "font-style: italic"]
    def getColorMapS0(self, module_ids):
        """ Standalone version - needed b/c of pickle problem """
        color_map = {}
        mod = len(MotifFormatter.COLORS)
        smod = len(MotifFormatter.STYLES)
        for module_id in module_ids: 
            ix = int(module_id)
            cur_color = ix % mod
            cur_style = int(round((ix / mod))) % smod
            style_str = """background-color: %s; %s; font-family: 'Courier New', Courier"""
            color_map[module_id] = style_str % (
                                MotifFormatter.COLORS[cur_color],
                                MotifFormatter.STYLES[cur_style])

        return color_map

    def getColorMap(self, motif_results):
        """ Return color mapping for motif_results """
        module_ids = []
        for motif in motif_results.Motifs:
            for module in motif.Modules:
                module_ids.append(module.ID)
        return self.getColorMapS0(sorted(module_ids))
    
    def getColorMapRgb(self, motif_results):
        """ Return color mapping for motif_results using RGB rather than hex.
        """
        module_ids = []
        for motif in motif_results.Motifs:
            for module in motif.Modules:
                module_ids.append(module.ID)
        color_map = {}
        mod = len(MotifFormatter.COLORS)
        for module_id in module_ids: 
            ix = int(module_id)
            cur_color = ix % mod
            color_map["color_" + str(module_id)] = \
                html_color_to_rgb(MotifFormatter.COLORS[cur_color])

        return color_map

    def __init__(self, *args):
        """Init method for MotifFormatter"""
        self.ConsCache={}
        self.ConservationThresh=None
    
    def __call__(self, *args):
        """Call method for MotifFormatter"""
        raise NotImplementedError
    
    def _make_conservation_consensus(self, module):
        """
        Return conservation consensus string
        """
        mod_id = module.ID
        if mod_id in self.ConsCache:
            return self.ConsCache[mod_id]

        cons_thresh = self.ConservationThresh

        cons_seq = ''.join(module.majorityConsensus())
        col_freqs = module.columnFreqs()
        cons_con_seq = []
        for ix, col in enumerate(col_freqs):
            col_sum = sum(col.values())
            keep = False
            for b, v in col.items():
                cur_cons = v / col_sum
                if cur_cons >= cons_thresh:
                    keep = True
            if keep:
                cons_con_seq.append(cons_seq[ix])
            else:
                cons_con_seq.append(" ")
        self.ConsCache[mod_id] = (cons_seq, ''.join(cons_con_seq))
        return self.ConsCache[mod_id]

    def _flag_conserved_consensus(self, cons_con_seq, cons_seq, cur_seq):
        """
        Annotate consensus  
        """
        color_style = """background-color: %s; font-family: 'Courier New', Courier"""

        span_fmt = """<span style="%s">%s</span>"""
        h_str = []
        for ix in range(len(cur_seq)):
            cur_c = cur_seq[ix]
            if cur_c == cons_con_seq[ix]:
                h_str.append(span_fmt % (color_style % "#eeeeee", "+"))
            elif cons_con_seq[ix] != " ":
                #h_str.append("<font color=red>-</font>")
                h_str.append(span_fmt % (color_style % "#ff0000", "-"))
            elif cons_seq[ix] == cur_c:
                #h_str.append("<font color=orange>*</font>")
                h_str.append(span_fmt % (color_style % "white", "*"))
            else:
                h_str.append("&nbsp;")
        return h_str 
        #return """<font face="Courier New, Courier, monospace">%s</font>""" % ''.join(h_str)

    
class MotifResults(object):
    """Object that holds a list of Modules, Motifs and a dict of Results.
    """

    def __init__(self,Modules=None, Motifs=None, Results=None, Parameters=None,
                 Alignment=None,MolType=None):
        """Initializes MotifResults object."""
        self.Modules = Modules or []
        self.Motifs = Motifs or []
        self.Results = Results or {} #Results not belonging to other categories.
        if Parameters:
            self.__dict__.update(Parameters)
        self.Alignment = Alignment
        self.MolType = MolType
    
    def makeModuleMap(self):
        """Returns dict of sequence ID keyed to modules.
        
            - result = {sequence_id:(index_in_sequence, module_id, module_len)}
        """
        module_map = {}  #Dict with locations of every motif keyed by module
        if self:
            for motif in self.Motifs:
                for module in motif.Modules:
                    mod_len = len(module)
                    mod_id = str(module.ID)
                    for skey, indexes in module.LocationDict.items():
                        if skey not in module_map:
                            module_map[skey] = []
                        for ix in indexes:
                            module_map[skey].append((ix, mod_id, mod_len))
        return module_map

def html_color_to_rgb(colorstring):
    """ convert #RRGGBB to an (R, G, B) tuple 
    
        - From Python Cookbook.
    """
    colorstring = colorstring.strip()
    if colorstring[0] == '#': colorstring = colorstring[1:]
    if len(colorstring) != 6:
        raise ValueError, "input #%s is not in #RRGGBB format" % colorstring
    r, g, b = colorstring[:2], colorstring[2:4], colorstring[4:]
    r, g, b = [int(n, 16) for n in (r, g, b)]
    #Divide each rgb value by 255.0 so to get float from 0.0-1.0 so colors
    # work in PyMOL
    r = r/255.0
    g = g/255.0
    b = b/255.0
    return (r, g, b)

def make_remap_dict(results_ids, allowed_ids):
    """Returns a dict mapping results_ids to allowed_ids.
    """
    remap_dict = {}
    warning = None
    if sorted(results_ids) == sorted(allowed_ids):
        remap_dict = dict(zip(results_ids,results_ids))
    else:
        warning = 'Sequence IDs do not match allowed IDs. IDs were remapped.'
        for ri in results_ids:
            curr_match = []
            for ai in allowed_ids:
                if ai.startswith(ri):
                    curr_match.append(ai)
            if not curr_match:
                raise ValueError, \
                    'Sequence ID "%s" was not found in allowed IDs'%(ri)
            #if current results id was prefix of more than one allowed ID
            elif len(curr_match)>1:
                #Check if any allowed ID matches map to other results IDs
                for cm in curr_match:
                    #Remove any matches that map to other results IDs
                    for ri2 in results_ids:
                        if ri2 != ri and cm.startswith(ri2):
                            curr_match.remove(cm)
                #Raise error if still more than one match
                if len(curr_match)>1:
                    raise ValueError, \
                        'Sequence ID "%s" had more than one match in allowed IDs: "%s"'%(ri,str(curr_match))
            remap_dict[ri]=curr_match[0]
    return remap_dict, warning