Crates.io | gene-extractor |
lib.rs | gene-extractor |
version | 0.1.0 |
source | src |
created_at | 2021-12-02 20:41:45.881715 |
updated_at | 2021-12-02 20:41:45.881715 |
description | Extract multiple genes in genomic contigs using reference fasta file |
homepage | https://github.com/hhandika/gene-extractor |
repository | https://github.com/hhandika/gene-extractor |
max_upload_size | |
id | 491417 |
size | 42,025 |
A command line app to extract gene from genomic contigs. The program requires phyluce and its dependencies to run. Future update may interact directly with Lastz, BWA-MEM or both.
genx
is a single executable command line app. The executable file will be available in the release link. Copy it to the folder that is registered in your PATH variable.
You can also install the app using the Rust package manager cargo:
cargo install genx
OS support:
Dependencies:
Phyluce and its depedencies (install here).
Subcommand options:
USAGE:
genx <SUBCOMMAND>
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
SUBCOMMANDS:
check Check dependencies
extract Batch gene tree estimation using IQ-Tree
help Prints this message or the help of the given subcommand(s)
Command options extract the gene:
USAGE:
genx extract --dir <PATH> --output <PATH> --refs <PATH>
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
OPTIONS:
-d, --dir <PATH> Path to contig directory
-o, --output <PATH> Path to output files
-r, --refs <PATH> Path to reference fasta files