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Implement scoring matrix downloading process #5

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Dec 5, 2024
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Implement scoring matrix downloading process #5

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fac7a6f
Implement scoring matrix downloading process
clonder Nov 19, 2024
62878f4
Update functions.py
clonder Nov 20, 2024
55ff60d
Added library resourses and fixed configuration file
clonder Nov 24, 2024
5a0734f
Changed the documentation for kinex init
clonder Nov 24, 2024
65f8d19
Deleted file
clonder Nov 24, 2024
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65 changes: 65 additions & 0 deletions =0.12.
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49 changes: 25 additions & 24 deletions docs/chapters/features/usage.rst
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Import package and initialise Kinex
Import Package and Initialize Kinex
===================================

1. Import kinex
1. **Import Kinex**

.. code:: python

from kinex import Kinex
from kinex import Kinex

2. Read the scoring matrix
2. **Create a Kinex Object**

- With Predefined Matrices:

It will look in the resources to find the matrices. If it doesn't find them, it will download them and save them for future use.

.. code:: python

scoring_matrix_ser_thr = pd.read_csv("https://zenodo.org/records/13964893/files/scoring_matrix_ser_thr_82k_sorted.csv.gz?download=1", compression="gzip")
scoring_matrix_tyr = pd.read_csv("https://zenodo.org/records/13964893/files/scoring_matrix_tyr_7k_sorted.csv.gz?download=1", compression="gzip")
scoring_matrix_ser_thr
kinex = Kinex()

- With Your Custom Matrices:

.. code:: python

AAK1 ACVR2A ... YSK4 ZAK
0 -11.147481 -6.325340 ... -6.723077 -7.402360
1 -10.421859 -6.178601 ... -6.343452 -7.373478
... ... ... ...
82753 8.074270 7.289390 ... 4.525527 4.837377
82754 8.623180 7.871226 ... 4.869195 5.062391
scoring_matrix_ser_thr = pd.read_csv("path/to/scoring_matrix_ser_thr.csv")
scoring_matrix_tyr = pd.read_csv("path/to/scoring_matrix_tyr.csv")

[82755 rows x 303 columns]
kinex = Kinex(scoring_matrix_ser_thr, scoring_matrix_tyr)

.. note::

You can optionally save the scoring matrix locally for faster use in the future.
The matrix looks like this:

.. code:: python

scoring_matrix_ser_thr.to_csv("scoring_matrix_ser_thr.csv")
scoring_matrix_tyr.to_csv("scoring_matrix_tyr.csv")
AAK1 ACVR2A ... YSK4 ZAK
0 -11.147481 -6.325340 ... -6.723077 -7.402360
1 -10.421859 -6.178601 ... -6.343452 -7.373478
... ... ... ...
82753 8.074270 7.289390 ... 4.525527 4.837377
82754 8.623180 7.871226 ... 4.869195 5.062391

Or just download using the links:
`https://zenodo.org/records/13964893/files/scoring_matrix_ser_thr_82k_sorted.csv.gz?download=1 <https://zenodo.org/records/13964893/files/scoring_matrix_ser_thr_82k_sorted.csv.gz?download=1>`_
`https://zenodo.org/records/13964893/files/scoring_matrix_tyr_7k_sorted.csv.gz?download=1 <https://zenodo.org/records/13964893/files/scoring_matrix_tyr_7k_sorted.csv.gz?download=1>`_

3. Create a kinex object
.. note::

.. code:: python
Predefined matrices can be found here:

kinex = Kinex(scoring_matrix_ser_thr, scoring_matrix_tyr)
- `Scoring Matrix for Serine/Threonine <https://zenodo.org/records/13964893/files/scoring_matrix_ser_thr_82k_sorted.csv.gz?download=1>`_
- `Scoring Matrix for Tyrosine <https://zenodo.org/records/13964893/files/scoring_matrix_tyr_7k_sorted.csv.gz?download=1>`_