# ensemblcov

- Complete set of multi-threaded genomics utilities for ensembl and differential expression matrix.

```
___   _ __    ___    ___   _ __ ___   | |__   | |   ___    ___   __   __
/ _ \ | '_ \  / __|  / _ \ | '_ ` _ \  | '_ \  | |  / __|  / _ \  \ \ / /
|  __/ | | | | \__ \ |  __/ | | | | | | | |_) | | | | (__  | (_) |  \ V /
\___| |_| |_| |___/  \___| |_| |_| |_| |_.__/  |_|  \___|  \___/    \_/


human genomics utilities.
    ************************************************
    Gaurav Sablok,
    Email: codeprog@icloud.com
   ************************************************

Usage: ensemblcov <COMMAND>

Commands:
threaded-auto           threaded version of ensembl auto gene conversion
auto-generate           autogenerate the ensemble gene conversion
gtf-annotate-generate   gtf file for annotation
countconvert            id convert from counts file
differentialexpression  id convert from differential expression
gene-ensembl            gene list extraction from ensembl
exon-ensembl            specific exons of the ensembl ids
help                    Print this message or the help of the given subcommand(s)

Options:
-h, --help     Print help
-V, --version  Print version
```

- before running the ensemlcov additional options, run one time,either autogenerate or threaded-generate to link the ensemblid to geneid.

```
ensemblcov  autogenerate yes
ensemblcov threaded-auto yes
ensemblcov countconvert ./sample-files/sample.matrix
ensemblcov differentialexpression ./sample-files/differntialresults.text
ensemblcov  gtf-annotate-generate ./sample-files/sample.gtf
ensemblcov gene-ensembl id.txt
ensemblcov exon-ensembl ./sample-files/idexon.txt
```

- To install windows version:
```
rustup component add llvm-tools
rustup target add x86_64-pc-windows-msvc
git clone https://github.com/IBCHgenomic/ensemblcov.git
cd ensemblcov
cargo xwin build --target x86_64-pc-windows-msvc
```

Gaurav Sablok
codeprog@icloud.com
