GeneVecTools 1.29

No project description provided

GeneVecTools

Reading in Variety of Genetic File Types

Vector Embedding Algorithms

Byte Array Encoders

Clustering and Preprocessing Steps for Compression

Similarity Search Tools for FASTA/FASTQ files

Installing

Tester files: https://tinyurl.com/cDNALibraryExampleFiles

.. code-block:: bash

pip install GeneVecTools

Usage

.. code-block:: bash

# import
>>> from GeneVecTools import SimSearch

.. code-block:: bash

"""
file is location of the "small_cDNA_Sequences_pbmc_1k_v2_S1_L002_R2_001.fastq" 
that you downloaded from https://tinyurl.com/cDNALibraryExampleFiles
if it is in current directory, just use file name
"""
>>> file = "small_cDNA_Sequences_pbmc_1k_v2_S1_L002_R2_001.fastq"

.. code-block:: bash

"""
f is the file location and name
length is the number of sequences we want in our scope
encoding is one of three choices: "one-hot-encoding", "standard", or "no-encoding"
bits is one of three choices: 2, 4, or 8
"""
>>> VECSS = SimSearch.VecSS(f=dir, length=10000, encoding="one-hot-encoding",bits=8)
>>> sequences = VECSS.readq()

.. code-block:: bash

# embed produces the vector embedding of the sequence
>>> embedded = VECSS.embed(VECSS.s)
>>> print(embedded)

.. code-block:: bash

"""
similarity search
D is the 
I is the 
time is the time it takes to perform this similarity search query
"""
>>> D, I, time = VECSS.run_search()
>>> print(D,I,time)

.. code-block:: bash

#Testing the embedding and umembedding process
>>> print(VECSS.unembed(VECSS.embed(VECSS.s)) == VECSS.s)

'True'