Physicochemical properties and indices for amino-acid sequences (ported from R).
Project description
peptides.py
Physicochemical properties and indices for amino-acid sequences.
🗺️ Overview
peptides.py
is a pure-Python package to compute common descriptors for
protein sequences. It is a port of Peptides
, the R package written by
Daniel Osorio for the same purpose.
This library has no external dependency and is available for all modern Python
versions (3.6+).
🔧 Installing
Install the peptides
package directly from PyPi
which hosts universal wheels that can be installed with pip
:
$ pip install peptides
💡 Example
Start by creating a Peptide
object from a protein sequence:
>>> import peptides
>>> peptide = peptides.Peptide("MLKKRFLGALAVATLLTLSFGTPVMAQSGSAVFTNEGVTPFAISYPGGGT")
Then use the appropriate methods to compute the descriptors you want:
>>> peptide.aliphatic_index()
89.8...
>>> peptide.boman()
-0.2097...
>>> peptide.charge(pH=7.4)
1.99199...
>>> peptide.isoelectric_point()
10.2436...
Methods that return more than one scalar value (for instance, Peptide.blosum_indices
)
will return a dedicated named tuple:
>>> peptide.ms_whim_scores()
MSWHIMScores(mswhim1=-0.436399..., mswhim2=0.4916..., mswhim3=-0.49200...)
Use the Peptide.descriptors
method to get a dictionary with every available
descriptor. This makes it very easy to create a pandas.DataFrame
with
descriptors for several protein sequences:
>>> seqs = ["SDKEVDEVDAALSDLEITLE", "ARQQNLFINFCLILIFLLLI", "EGVNDNECEGFFSAR"]
>>> df = pandas.DataFrame([ peptides.Peptide(s).descriptors() for s in seqs ])
>>> df
BLOSUM1 BLOSUM2 BLOSUM3 BLOSUM4 ... Z2 Z3 Z4 Z5
0 0.367000 -0.436000 -0.239 0.014500 ... -0.711000 -0.104500 -1.486500 0.429500
1 -0.697500 -0.372500 -0.493 0.157000 ... -0.307500 -0.627500 -0.450500 0.362000
2 0.479333 -0.001333 0.138 0.228667 ... -0.299333 0.465333 -0.976667 0.023333
[3 rows x 66 columns]
💭 Feedback
⚠️ Issue Tracker
Found a bug ? Have an enhancement request ? Head over to the GitHub issue tracker if you need to report or ask something. If you are filing in on a bug, please include as much information as you can about the issue, and try to recreate the same bug in a simple, easily reproducible situation.
🏗️ Contributing
Contributions are more than welcome! See
CONTRIBUTING.md
for more details.
⚖️ License
This library is provided under the GNU General Public License v3.0.
The original R Peptides
package was written by Daniel Osorio,
Paola Rondón-Villarreal and
Rodrigo Torres, and is licensed under
the terms of the GPLv2.
This project is in no way not affiliated, sponsored, or otherwise endorsed
by the original Peptides
authors. It was developed
by Martin Larralde during his PhD project
at the European Molecular Biology Laboratory in
the Zeller team.
Project details
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