diff --git a/rpg/digest.py b/rpg/digest.py index 383c008e0172296fb283375a577f084a230efb8c..bebe5796f85ba72582067f081dd859456772fdf5 100644 --- a/rpg/digest.py +++ b/rpg/digest.py @@ -35,7 +35,7 @@ class ResultOneDigestion: :param enzyme_name: name of the enzyme used :param peptides: all resulting peptides after digestion :param nb_cleavage: number of cleavage that occurs - :param pos_miss_cleavage: position of miss-cleavage that occurs + :param pos_miss_cleavage: position of miscleavage that occurs :type enzyme_name: str :type peptides: list(:py:class:`~rpg.sequence.Peptide`) :type nb_cleavage: int @@ -55,10 +55,10 @@ class ResultOneDigestion: # self representation for print def __repr__(self): return "Number of cleavage: " + str(self.nb_cleavage) + \ - "\nNumber of miss-cleavage: " + \ + "\nNumber of miscleavage: " + \ str(len(self.pos_miss_cleavage)) + \ - "\nPositions of miss-cleavage: " + str(self.pos_miss_cleavage)\ - + "\nRatio of miss-cleavage: " + \ + "\nPositions of miscleavage: " + str(self.pos_miss_cleavage)\ + + "\nRatio of miscleavage: " + \ str(self.get_ratio_miss_cleavage()) + \ "\nPeptides: " + str(self.peptides) + "\n" @@ -102,26 +102,26 @@ class ResultOneDigestion: self.nb_cleavage += 1 def get_nb_miss_cleavage(self): - """Get the number of miss-cleavages that occurs + """Get the number of miscleavages that occurs on this digestion. - :return: number of miss-cleavage + :return: number of miscleavage :rtype: int """ return len(self.pos_miss_cleavage) def add_miss_cleavage(self, new_pos_miss_cleavage): - """Add a miss-cleavage to :attr:`self.pos_miss_cleavage`. + """Add a miscleavage to :attr:`self.pos_miss_cleavage`. - :param new_pos_miss_cleavage: position of miss-cleavage + :param new_pos_miss_cleavage: position of miscleavage :type new_pos_miss_cleavage: int """ self.pos_miss_cleavage.append(new_pos_miss_cleavage) def get_ratio_miss_cleavage(self): - """Get ratio of miss-cleavage. + """Get ratio of miscleavage. - :return: ratio of miss-cleavage + :return: ratio of miscleavage :rtype: float """ ret = 0 @@ -132,9 +132,9 @@ class ResultOneDigestion: return ret def get_miss_cleavage_pos(self): - """Get positions of miss-cleavage as a string. + """Get positions of miscleavage as a string. - :return: positions of miss-cleavage + :return: positions of miscleavage :rtype: str """ ret = "" @@ -186,7 +186,7 @@ class ResultOneDigestion: def get_more_info(self): """Return informations and statistics about this digestion, - *i.e.* number of (miss)-cleavages and positions, miss-cleavage + *i.e.* number of (miss)-cleavages and positions, miscleavage ratio, size of the smallest peptide and first and last peptide. :return: informations and statistics ready to be printed @@ -195,10 +195,10 @@ class ResultOneDigestion: ret = "" ret += "\nNumber of cleavage: " + str(self.nb_cleavage) + "\n" ret += "Cleavage position: " + self.get_cleavage_pos() + "\n" - ret += "Number of miss-cleavage: " + str(self.get_nb_miss_cleavage())\ + ret += "Number of miscleavage: " + str(self.get_nb_miss_cleavage())\ + "\n" - ret += "Miss-cleavage position: " + self.get_miss_cleavage_pos() + "\n" - ret += "Miss-cleavage ratio: %.2f%%\n" % self.get_ratio_miss_cleavage() + ret += "miscleavage position: " + self.get_miss_cleavage_pos() + "\n" + ret += "miscleavage ratio: %.2f%%\n" % self.get_ratio_miss_cleavage() ret += "Smallest peptide size: " + \ str(self.get_smallest_peptide().size) + "\n" ret += "N terminal peptide: " + self.peptides[0].sequence + "\n" @@ -250,9 +250,9 @@ def one_digest(pep, enz): for rul in enz.rules: # Apply the rule: if we need to cut if rule.handle_rule(pep.sequence, pos, rul, cut): - # Random to handle miss-cleavage + # Random to handle miscleavage tmp_rand = random.random() * 100 - # Rand > ratio_miss_cleavage, no miss-cleavage occurs + # Rand > ratio_miss_cleavage, no miscleavage occurs if tmp_rand > enz.ratio_miss_cleavage: # Test, this should NEVER be used if rul.pos == -1: @@ -283,7 +283,7 @@ def one_digest(pep, enz): a_cut_occurs = True # A cleavage occur ret.inc_nb_cleavage() - # A miss-cleavage occurs + # A miscleavage occurs else: ret.add_miss_cleavage(pos) # End of the peptide