Translate nucleic acid sequences to their corresponding peptide sequences. Like EMBOSS transeq, but written in go
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
download the latest binary from the release page
or install with go get (require to have go installed on your machine)
go get -u "github.com/feliixx/gotranseq"
use gotranseq --help to print the help:
gotranseq version 0.1
Usage:
gotranseq
required:
-s, --sequence=<filename> Nucleotide sequence(s) filename
-o, --outseq=<filename> Protein sequence filename
optional:
-f, --frame=<code> 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=<code> 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=<n> Number of threads to use, default is number of CPU
general:
-h, --help Show this help message
-v, --version Print the tool version and exit