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A point mutation analyzing tool for nucleotide sequence

Project description

Latest PyPI version Latest Travis CI build status

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 ./ install


  • Python >= 2.7
  • biopython


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

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))


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


bio-pm was written by Ekeyme Mo.

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