compbiolab-CLI 0.2.3

CLI tool for CS410 project

CLI

Table Of Contents

• Table of Contents
• Software Info
• Overview
• Installation
• Usage
  • Comparing protein sequences
    • Comparing Arguments
  • Searching
    • Searching Arguments
• Available Metrics
• Examples

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

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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