https://github.com/camilogarciabotero/bioatomscount.jl

Count organic atoms in a BioSequence
https://github.com/camilogarciabotero/bioatomscount.jl

atoms bioinformatics biojulia organic

Last synced: about 1 month ago
JSON representation

Count organic atoms in a BioSequence

• Host: GitHub
• URL: https://github.com/camilogarciabotero/bioatomscount.jl
• Owner: camilogarciabotero
• License: mit
• Created: 2024-08-14T21:25:49.000Z (8 months ago)
• Default Branch: main
• Last Pushed: 2024-11-18T02:32:55.000Z (5 months ago)
• Last Synced: 2025-01-20T16:56:52.908Z (3 months ago)
• Topics: atoms, bioinformatics, biojulia, organic
• Language: Julia
• Homepage: https://camilogarciabotero.github.io/BioAtomsCount.jl/
• Size: 257 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# BioAtomsCount



  


  Counting BioSequences' atoms 







[![Documentation](https://img.shields.io/badge/documentation-online-blue.svg?logo=Julia&logoColor=white)](https://camilogarciabotero.github.io/BioAtomsCount.jl/dev/)

[![Latest Release](https://img.shields.io/github/release/camilogarciabotero/BioAtomsCount.jl.svg)](https://github.com/camilogarciabotero/BioAtomsCount.jl/releases/latest)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13631113.svg)](https://doi.org/10.5281/zenodo.13631113)




[![CI Workflow](https://github.com/camilogarciabotero/BioAtomsCount.jl/actions/workflows/CI.yml/badge.svg)](https://github.com/camilogarciabotero/BioAtomsCount.jl/actions/workflows/CI.yml)

[![License](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/camilogarciabotero/BioAtomsCount.jl/blob/main/LICENSE)

[![Work in Progress](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)

[![Downloads](https://img.shields.io/badge/dynamic/json?url=http%3A%2F%2Fjuliapkgstats.com%2Fapi%2Fv1%2Fmonthly_downloads%2FBioAtomsCount&query=total_requests&suffix=%2Fmonth&label=Downloads)](http://juliapkgstats.com/pkg/BioAtomsCount)

[![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)

[![JET](https://img.shields.io/badge/%E2%9C%88%EF%B8%8F%20tested%20with%20-%20JET.jl%20-%20red)](https://github.com/aviatesk/JET.jl)



> This is a *fast* and *lightweight* package that counts the number of atoms in a given `BioSequence` object. It was inspired by the [Biocost.jl](https://github.com/juanvillada/Biocost.jl/tree/main) package.

## Installation



BioAtomsCount is a  

    

        

        Julia Language

    

      package. To install BioAtomsCount,

    please open

    Julia's interactive session (known as REPL) and press ]

    key in the REPL to use the package mode, then type the following command



```julia

pkg> add BioAtomsCount

```

## Usage

The `BioAtomsCount` module exports a single function `countatoms` which takes a `BioSequence` object as input and returns a matrix of the count of atoms in the sequence.

Each column of the matrix corresponds to a different atom (C, H, N, O) for DNA and (C, H, N, O, S) for proteins and each row corresponds to a different residue in the sequence.

Here is an example of a DNA sequence:

```julia

using BioSequences

phi = dna"GTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCAGAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGA"

countatoms(phi)

4×4 Matrix{Int64}:

#   C     H     N     O    

 6455  6455  6455     0  # A

 4628  5785  3471  1157  # C

 6270  6270  6270  1254  # G

 8420  8420  3368  3368  # T

```

Now an example of a protein sequence:

```julia

lambdaprotein = aa"MEVNKKQLADIFGASIRTIQNWQEQGMPVLRGGGKGNEVLYDSAAVIKWYAERDAEIENEKLRREVEELRQASEADLQPGTIEYERHRLTRAQADAQELKNARDSAEVVETAFCTFVLSRIAGEIASILDGLPLSVQRRFPELENRHVDFLKRDIIKAMNKAAALDELIPGLLSEYIEQSG*"

countatoms(lambdaprotein)

20×5 Matrix{Int64}:

#  C    H   N   O  S

  60  140  20  40  0  # A (Ala)

  90  210  60  30  0  # R (Arg)

  28   56  14  21  0  # N (Asn)

  40   70  10  40  0  # D (Asp)

   3    7   1   2  1  # C (Cys)

  50   90  10  40  0  # Q (Gln)

 110  220  44  66  0  # E (Glu)

  22   55  11  22  0  # G (Gly)

  12   18   6   4  0  # H (His)

  78  169  13  26  0  # I (Ile)

 108  234  18  36  0  # L (Leu)

  54  126  18  18  0  # K (Lys)

  15   33   3   6  3  # M (Met)

  45   55   5  10  0  # F (Phe)

  25   45   5  10  0  # P (Pro)

  27   63   9  27  0  # S (Ser)

  20   45   5  15  0  # T (Thr)

  22   24   4   4  0  # W (Trp)

  36   44   4  12  0  # Y (Tyr)

  50  110  10  20  0  # V (Val)

```

Sometimes what is needed is the total number of each atom in the sequence. This can be achieved by a simple sum of the matrix:

```julia

counts = countatoms(lambdaprotein)

sum(counts, dims=1)

1×5 Matrix{Int64}:

#  C     H    N    O  S

 895  1814  270  449  4

```

## License

MIT License