bio-pm

A point mutation analyzing tool for nucleotide sequence

Installation

Install through pip:

pip install bio-pm

Or manually (assuming all required modules are installed on your system):

python ./setup.py install

Requirements

• Python >= 2.7
• biopython

Examples

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 pm.status objects

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

Licence

MIT licensed. See the bundled LICENSE file for more details.

Authors

bio-pm was written by Ekeyme Mo.