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 Works on Linux, Mac and windows
Download the binary from the release page
or
Build from source:
First, make sure that go is installed on your machine (see install go for details ). Then clone the repo and build it:
git clone https://github.com/feliixx/gotranseq.git cd gotranseq go build use gotranseq --help to print the help:
gotranseq version 0.3.0 Usage: gotranseq --sequence file.fna --outseq out.faa 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 worker to use (default: number of CPU) general: -h, --help Show this help message -v, --version Print the tool version and exit