CLI tool for CS410 project
Project description
CLI
Table Of Contents
Software Info:
Software Name: CompBioLab CLI
Latest Software Version: v0.2.3
PyPI: https://pypi.org/project/compbiolab-CLI/
Overview
Our goal for this project is to read a new input sequence and find the protein family which it belongs in by comparing it with existing sequences in the database. In addition to finding the closest family for a new sequence, our search application can also accept an autoencoded fingerprint and see which family is the best match using a variety of different metrics.
Our compare application allows different protein families to be compared directly using different distance functions. It accepts the names of families already in the database, but it can also accept files containing data from new latent spaces.
The program can be downloaded from PyPI (the Python Package Index), and it has a Command Line Interface.
Installation
pip install compbiolab-CLI
Usage
Comparing protein sequences
Find the distance between fingerprints of two protein families
compare [-h] [-names SHOW_NAMES_BOOL] [-n1 FIRST_FAMILY] [-n2 SECOND_FAMILY] [-nl1 NL1] [-nl2 NL2] [-m DISTANCE_METRIC] [-p P_NORM] [-out OUTPUT_FILE] [-of OUTPUT_FORMAT] [-om OUTPUT_MODE]
Comparing Arguments
-
-names
Boolean, Show available protein family names
-
-n1
First family's name
-
-n2
Second family's name
-
-nl1
The file name of the first new latent space. Provide a new protein family latent space to compare it with one of the existing protein families or with the second new latent space. The file should contain 30 floats, each float in a separate line.
-
-nl2
The file name of the second new latent space. Provide a new protein family latent space to compare it with one of the existing protein families or with the first new latent space. The file should contain 30 floats, each float in a separate line.
-
-m
[optional] Distance metric. Default: euclidean
-
-p
[optional] Scalar, The p-norm to apply for Minkowski, weighted and unweighted. Default: 2
-
-out
[optional] Output filename
-
-of
[optional] Output format, text or csv. Default: text
-
-om
[optional] Output mode, a[ppend] or w[rite]. Default: a
Searching
Find the closest family to a new protein sequence
search [-h] [-names SHOW_NAMES_BOOL] [-m DISTANCE_METRIC] [-p P_NORM] [-nl1 NL1] [-nl2 NL2] [-ns NS] [-out OUTPUT_FILE] [-of OUTPUT_FORMAT] [-om OUTPUT_MODE]
Searching Arguments
-
-names
Boolean, Show available protein family names
-
-nl1
The file name of a new latent space. Provide a new protein family latent space. The closest protein family to this new latent space will be shown.
-
-nl2
The file name of a new latent space. Provide a new protein family latent space. The closest protein family to this new latent space will be shown.
-
-ns
The name of the file containing a protein sequence. Provide a protein sequence to get the closest protein family for this sequence.
-
-m
[optional] Distance metric. Default: euclidean
-
-p
[optional] Scalar, The p-norm to apply for Minkowski, weighted and unweighted. Default: 2
-
-out
[optional] Output filename
-
-of
[optional] Output format, text or csv. Default: text
-
-om
[optional] Output mode, a[ppend] or w[rite]. Default: a
Available metrics
euclidean (default), minkowski, cityblock, sqeuclidean, cosine, correlation, hamming, jaccard, chebyshev, canberra, braycurtis, yule, dice, kulsinski, rogerstanimoto, russellrao, sokalmichener, sokalsneath
Examples
To see all the available protein families, run command:
compare -names
You can find the Euclidean distance between two families ATKA_ATKC and CDSA_RSEP by running the command:
compare -n1 ATKA_ATKC -n2 CDSA_RSEP
If you want to find the Cityblock distance between ATKA_ATKC and a new latent space stored at second_new_latent_example.txt, you can run the command:
compare -n1 ATKA_ATKC -nl2 second_new_latent_example.txt -m cityblock
If you want to find the cosine distance between two new latent spaces stored at first_new_latent_example.txt and second_new_latent_example.txt, you can run the command:
compare -nl1 first_new_latent_example.txt -nl2 second_new_latent_example.txt -m cityblock
You can find the closest protein family to first_new_latent_example.txt in cosine distance by running the command:
search -nl1 first_new_latent_example.txt -m cosine
You can find the closest family to a new protein sequence (for example new_sequence_example.txt) by running:
search -ns new_sequence_example.txt
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