compbiolab-CLI 0.1.2

CLI tool for CS410 project

CLI

CompBioLabCLI

CLI tool for CS410 project (compbiolab)

Overview

Our goal for this project is to read a new input sequence and find the protein family in which it belongs to by comparing it with existing sequences in the database. We can also read two different inputs sequences and compare them to find the similarities between the two. The program can be downloaded from PyPI (Python Package Index) via the Instructions below and will have a Command Line Interface.

1. Find the distance between fingerprints of two protein families.
2. Find the closest family to a new protein sequence.

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]

Arguments

• -names

  Boolean, Show available protein family names

• -n1

  First family's name

• -n2

  Second family's name

• -nl1

  [optional] 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

  [optional] 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] [-out OUTPUT_FILE] [-of OUTPUT_FORMAT] [-om OUTPUT_MODE]

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.

• -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 1

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