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| from sequence import Sequence | |
| class DNAseq(Sequence): | |
| def get_base_counts(self): | |
| base_counts = { | |
| 'a': self.get_unit_count('a'), | |
| 't': self.get_unit_count('t'), | |
| 'g': self.get_unit_count('g'), | |
| 'c': self.get_unit_count('c'), | |
| } | |
| return base_counts | |
| # Total number of each base within the sequence returned as a dictionary | |
| def get_base_percentages(self): | |
| base_percentages = { | |
| 'a': self.get_unit_percentage('a'), | |
| 't': self.get_unit_percentage('t'), | |
| 'g': self.get_unit_percentage('g'), | |
| 'c': self.get_unit_percentage('c'), | |
| } | |
| return base_percentages | |
| # Base content percentage for each base returned as a dictionary | |
| def get_gc_content(self): | |
| total_bases = self.get_seq_length() | |
| gc_count = self.sequence.count('g') + self.sequence.count('c') | |
| gc_content = (gc_count / total_bases) * 100 | |
| return gc_content | |
| # Guanine Cytosine (gc) content by percentage | |
| def get_at_content(self): | |
| total_bases = self.get_seq_length() | |
| at_count = self.sequence.count('a') + self.sequence.count('t') | |
| at_content = (at_count / total_bases) * 100 | |
| return at_content | |
| # Adenine Thymine (at) content by percentage | |
| def get_purine_content(self): | |
| total_bases = self.get_seq_length() | |
| ag_count = self.sequence.count('a') + self.sequence.count('g') | |
| ag_content = (ag_count / total_bases) * 100 | |
| return ag_content | |
| # Adenine Guanine (purine) content by percentage | |
| def get_pyrimidine_content(self): | |
| total_bases = self.get_seq_length() | |
| ct_count = self.sequence.count('c') + self.sequence.count('t') | |
| ct_content = (ct_count / total_bases) * 100 | |
| return ct_content | |
| # Cytosine Thymine (pyrimidine) content by percentage | |