/usr/share/pyshared/cogent/motif/util.py is in python-cogent 1.5.3-2.
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"""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 2007-2012, The Cogent Project"
__credits__ = ["Jeremy Widmann", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.3"
__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(" ")
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
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