#!/usr/bin/env python # # ModelingRecipe # # ModelingRecipe sorts alignment positions into different boxes (1 box == 1 operation, e.g. copying residues) # # http://iimcb.genesilico.pl/moderna/ # __author__ = "Magdalena Rother, Tomasz Puton, Kristian Rother" __copyright__ = "Copyright 2008, The Moderna Project" __credits__ = ["Janusz Bujnicki"] __license__ = "GPL" __maintainer__ = "Magdalena Rother" __email__ = "rother.magdalena@gmail.com" __status__ = "Production" import os from rna_tools.tools.mini_moderna3.moderna.sequence.RNAAlignment import RNAAlignmentParser, DEFAULT_SHRINK from rna_tools.tools.mini_moderna3.moderna.Constants import STANDARD_BASES from rna_tools.tools.mini_moderna3.moderna.util.Errors import AlignmentError from rna_tools.tools.mini_moderna3.moderna.util.LogFile import log MODES = ['has_gap', 'is_mismatch', 'has_template_gap', \ 'has_target_gap', 'is_unidentified'] class ModelingRecipe(object): """ """ def __init__(self): self.copy = [] self.copy_backbone = [] self.exchange = [] self.remove_modifications = [] self.add_modifications = [] self.add_fragment = [] self.difficult = [] # ??? report that an user should see this self.add_fragment_5p = [] self.add_fragment_3p = [] # MR: PROPOSAL: make orer of modeling_tasks flexible. #self.order = {'copy_backbone': 1, ...} # def set_order class RecipeMaker(object): """ All AlignmentPosition instances from an alignment are packed into boxes which represent tasks for modeling. There are fallowing boxes: - copy ---> the same template and target letter and no ANY_RESIDUE - copy_backbone ---> target and template letter are present and one or two of them are ANY_RESIDUE - exchange ---> target and template letter are present and different and not ANY_RESIDUE - remove_modifications ---> template and target letters are present and template residue is not a standard one - add_modification ---> template and target letters are present and target residue is not a standard one - add_fragment ---> ther is no template or no target (never both) letter, this positions belongs to gap that doesn't have any other gap in target or template in distance less than 2 - difficult ---> gaps different than above """ def __init__(self, alignment): self.recipe = ModelingRecipe() self.alignment = alignment self.set_alignment_properties() def get_differences (self, mode='is_different'): """ Returns these positions in alignment which are different in a given sequences as a list of AlignmentPosition instances. Arguments: - mode (by default 'all') Modes: - 'is_different' - all differences are taken into account ('mismatch','gap in template','gap in target') - 'has_gap' - only gaps in template and gaps in target - 'has_template_gap' - 'has_target_gap' - 'is_mismatch' - 'is_unidentified' - when one of letters or both is ANY_RESIDUE """ differences = [] if mode in MODES: for apos in self.alignment: method = getattr(apos, mode) if method(): differences.append(apos) return differences raise AlignmentError("Bad mode type. Should be one of %s."%str(MODES)) def remove_ap_from_box(self, apos): """ Removes given AlignmentPosition from given boxes. By defult removes apos from all boxes besides add_fragment ons. """ if apos in self.recipe.copy: self.recipe.copy.remove(apos) if apos in self.recipe.copy_backbone: self.recipe.copy_backbone.remove(apos) if apos in self.recipe.exchange: self.recipe.exchange.remove(apos) if apos in self.recipe.add_modifications: self.recipe.add_modifications.remove(apos) if apos in self.recipe.remove_modifications: self.recipe.remove_modifications.remove(apos) if apos in self.recipe.add_fragment: self.recipe.add_fragment.remove(apos) if apos in self.recipe.add_fragment_5p: self.recipe.add_fragment_5p.remove(apos) if apos in self.recipe.add_fragment_3p: self.recipe.add_fragment_3p.remove(apos) if apos in self.recipe.difficult: self.recipe.difficult.remove(apos) #TODO is this used? def segregate_gaps(self, gaps_devided): """ Segregate given gaps list into proper boxes (add_fragmen, add_fragment_5p, add_fragment_3p, difficult). """ for gap in gaps_devided: # gap is a tuple of ap belonging to one gap # ALL STRANGE CASES AT THE BEGINING AND AT THE END OF THE ALIGNMENT if gap[0].alignment_position == 1: # gap at beginning of alignment if gap[0].target_letter: self.recipe.add_fragment_5p.append(gap) elif gap[0].alignment_position == 2: # gap at the second position in the alignment ap_1before = self.alignment[gap[0].alignment_position -1] if gap[0].target_letter and ap_1before.target_letter: # AA # A- self.remove_ap_from_box(ap_1before) self.recipe.add_fragment_5p.append([ap_1before]+ gap) elif gap[0].target_letter and ap_1before.template_letter: # -A # A- self.recipe.add_fragment_5p.append(gap) elif ap_1before.target_letter and ap_1before.template_letter: # A- # AA self.remove_ap_from_box(ap_1before) self.recipe.add_fragment_5p.append([ap_1before]) elif gap[-1].alignment_position == len(self.alignment): # gap at end of alignment if gap[0].target_letter: self.recipe.add_fragment_3p.append(gap) elif gap[-1].alignment_position == len(self.alignment)-1: # gap at the second position before the end of the alignment ap_1after = self.alignment[len(self.alignment)] if gap[-1].target_letter and ap_1after.target_letter: # AA # -A self.remove_ap_from_box(ap_1after) self.recipe.add_fragment_3p.append(gap+[ap_1after]) elif gap[-1].target_letter and ap_1after.template_letter: # A- # -A self.recipe.add_fragment_3p.append(gap) elif ap_1after.target_letter and ap_1after.template_letter: # AA # -A self.remove_ap_from_box(ap_1after) self.recipe.add_fragment_3p.append([ap_1after]) # REGULAR GAPS IN THE MIDDLE OF THE ALIGNMENT else: ap_1before = self.alignment[gap[0].alignment_position -1] ap_2before = self.alignment[gap[0].alignment_position -2] ap_1after = self.alignment[gap[-1].alignment_position +1] ap_2after = self.alignment[gap[-1].alignment_position +2] #if ap_1before.is_different('gap') or ap_2before.is_different('gap') \ #or ap_1after.is_different('gap') or ap_2after.is_different('gap'): if ap_1before.has_gap() or ap_1after.has_gap(): self.recipe.difficult.append(gap) #self.difficult.append(gap) # MM CHANGES: elif ap_2before.has_gap() or ap_2after.has_gap(): self.recipe.add_fragment.append([ap_1before] + gap + [ap_1after]) #TODO: too long gaps should remain difficult #TODO: gaps close to each other should be inserted, # but with one base less cut on each side. # --> also else: self.recipe.add_fragment.append([ap_2before, ap_1before] + gap + [ap_1after, ap_2after]) def set_add_fragment_property(self, mode='has_template_gap'): """ Fill in add_fragment an difficult propertis. """ gaps = self.get_differences(mode) if gaps: gaps2 = [ap.alignment_position for ap in gaps] # list of int gaps_devided = [] # nested list of int gaps2.sort() counter = gaps2[0] new_gap = [] # group gaps for num in gaps2: if num == counter: # same gap new_gap.append(self.alignment[num]) counter += 1 else: # new gap gaps_devided.append(new_gap) new_gap = [] new_gap.append(self.alignment[num]) counter = num+1 if new_gap: gaps_devided.append(new_gap) if gaps_devided: self.segregate_gaps(gaps_devided) def set_alignment_properties(self): """ Fill in alignment 'boxes'. See class description. """ self.recipe.copy = self.alignment.get_identical_positions() self.recipe.copy_backbone = self.get_differences('is_unidentified') differences = self.get_differences('is_mismatch') self.recipe.exchange = [ap for ap in differences if ap.target_letter.long_abbrev in STANDARD_BASES and ap.template_letter.long_abbrev in STANDARD_BASES] self.recipe.add_modifications = [ap for ap in differences if ap.target_letter.long_abbrev not in STANDARD_BASES] self.recipe.remove_modifications = [ap for ap in differences if ap.target_letter.long_abbrev in STANDARD_BASES and ap.template_letter.long_abbrev not in STANDARD_BASES] self.set_add_fragment_property('has_template_gap') self.set_add_fragment_property('has_target_gap')