A point mutation analyzing tool for nucleotide sequence
Install through pip:
pip install bio-pm
Or manually (assuming all required modules are installed on your system):
python ./setup.py install
- Python >= 2.7
Analyze point mutation status using
pm.analyze(seq, stdseq, translate=True)
>>> import pm >>> >>> stdseq = 'ATGGGCGC' >>> seq_with_gap = 'ATGGGCG-C' >>> pm.analyze(seq_with_gap, stdseq) <pm.status.NA object with: gaps=1, nt_pm=1, aa_pm=0, stdseq='ATGGGCGC'> >>>
Quickly compare between
p.status objects with same stdseqs have their internal order. That is
Y > Conserved >
PM > NA.
>>> import pm >>> >>> stdseq = "ATGGGCGCT" >>> seq_without_pm = 'ATGGGCGCT' >>> seq_conserved = "ATGGGCGCC" >>> seq_with_pm = 'ATGGGCGAT' >>> status_Y = pm.analyze(seq_without_pm, stdseq) >>> status_Conserved = pm.analyze(seq_conserved, stdseq) >>> status_PM = pm.analyze(seq_with_pm, stdseq) >>> >>> status_Y > status_Conserved > status_PM True >>>
Help generate HGVS-like mutation format
Codes continues from
Quickly compare the point mutation status objects
>>> from pm.pattern import mutant_to_str >>> >>> status_PM.pattern <pm.pattern.TranslatedPattern object at 0x2b03c9cfdc18> >>> >>> for nt_pm, aa_pm in status_PM.pattern.list(): ... print(mutant_to_str(*nt_pm) + '|' + mutant_to_str(*aa_pm)) ... 8C>A|3A>D
MIT licensed. See the bundled LICENSE file for more details.
bio-pm was written by Ekeyme Mo.