Skip to main content

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

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 >= 3
  • biopython

Examples

Analyze point mutation status using pm.analyze(seq, stdseq, translate=True)

>>> import pm
>>>
>>> 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.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

bio-pm-0.1.0.tar.gz (14.6 kB view hashes)

Uploaded source

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page