https://github.com/feliixx/gotranseq

convert nucleic sequence in protein sequence
https://github.com/feliixx/gotranseq

bioinformatics dna go protein-sequences translation

Last synced: 26 days ago
JSON representation

convert nucleic sequence in protein sequence

• Host: GitHub
• URL: https://github.com/feliixx/gotranseq
• Owner: feliixx
• License: mit
• Created: 2017-10-11T14:10:48.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2023-02-02T19:56:10.000Z (over 1 year ago)
• Last Synced: 2024-05-01T14:41:46.055Z (about 2 months ago)
• Topics: bioinformatics, dna, go, protein-sequences, translation
• Language: Go
• Size: 3 MB
• Stars: 17
• Watchers: 3
• Forks: 9
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Lists

• awesome-bio-go - Gotranseq

README

        
[![Go Report Card](https://goreportcard.com/badge/github.com/feliixx/gotranseq)](https://goreportcard.com/report/github.com/feliixx/gotranseq)

[![codecov](https://codecov.io/gh/feliixx/gotranseq/branch/master/graph/badge.svg)](https://codecov.io/gh/feliixx/gotranseq)

[![PkgGoDev](https://pkg.go.dev/badge/github.com/feliixx/gotranseq/transeq)](https://pkg.go.dev/github.com/feliixx/gotranseq/transeq)

# Gotranseq

Translate nucleic acid sequences to their corresponding peptide sequences. 

Like EMBOSS transeq, but written in go 

## Purpose 

EMBOSS transeq is a great tool, but can be quite painfull for some use cases, 

because it silently truncate the sequence ID if it contains chars like **':'**, 

or rename the sequence ID if it contains chars like **'|'**

This tool is an attempt to solve this problem. It's also way faster than EMBOSS

transeq because it can be parrallelized: 

benchmark on ubuntu 16.04, machine with 2 CPU Intel(R) Core(TM)2 Duo CPU 3.00GHz

with a 189MB fasta file: 

```

#EMBOSS transeq

time transeq -sequence file.fna -outseq out.faa -frame 6  

41,82s user 0,76s system 85% cpu 49,696 total

#gotranseq

time ./gotranseq --sequence file.fna --outseq out.faa --frame 6 -n 2

7,75s user 0,98s system 159% cpu 5,472 total

```

Works on Linux, Mac and windows

## Installation

Download the binary from the [release page](https://github.com/feliixx/gotranseq/releases)

or

Build from source:

First, make sure that go is installed on your machine (see [install go](https://golang.org/doc/install) for details ). Then clone the repo and build it:

```

git clone https://github.com/feliixx/gotranseq.git

cd gotranseq

go build

```

## Usage 

use `gotranseq --help` to print the help: 

```

gotranseq version 0.3.0

Usage:

  gotranseq --sequence file.fna --outseq out.faa

required:

  -s, --sequence=    Nucleotide sequence(s) filename

  -o, --outseq=      Protein sequence filename

optional:

  -f, --frame=           Frame to translate. Possible values:

                               [1, 2, 3, F, -1, -2, -3, R, 6]

                               F: forward three frames

                               R: reverse three frames

                               6: all 6 frames

                               (default: 1)

  -t, --table=           NCBI code to use, see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?chapter=tgencodes#SG1 for

                               details. Available codes:

                               0: Standard code

                               2: The Vertebrate Mitochondrial Code

                               3: The Yeast Mitochondrial Code

                               4: The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code

                               5: The Invertebrate Mitochondrial Code

                               6: The Ciliate, Dasycladacean and Hexamita Nuclear Code

                               9: The Echinoderm and Flatworm Mitochondrial Code

                               10: The Euplotid Nuclear Code

                               11: The Bacterial, Archaeal and Plant Plastid Code

                               12: The Alternative Yeast Nuclear Code

                               13: The Ascidian Mitochondrial Code

                               14: The Alternative Flatworm Mitochondrial Code

                               16: Chlorophycean Mitochondrial Code

                               21: Trematode Mitochondrial Code

                               22: Scenedesmus obliquus Mitochondrial Code

                               23: Thraustochytrium Mitochondrial Code

                               24: Pterobranchia Mitochondrial Code

                               25: Candidate Division SR1 and Gracilibacteria Code

                               26: Pachysolen tannophilus Nuclear Code

                               29: Mesodinium Nuclear

                               30: Peritrich Nuclear

                               (default: 0)

  -c, --clean                  Replace stop codon '*' by 'X'

  -a, --alternative            Define frame '-1' as using the set of codons starting with the last codon of the sequence

  -T, --trim                   Removes all 'X' and '*' characters from the right end of the translation. The trimming process starts at the

                               end and continues until the next character is not a 'X' or a '*'

  -n, --numcpu=             Number of worker to use (default: number of CPU)


general:

  -h, --help                   Show this help message

  -v, --version                Print the tool version and exit

```