get-gene-info.pl

Retrieving HGNC gene symbol reports (human genes only) via a list of gene IDs. (mac or linux compatible only).

SYNOPSIS

./get-gene-info.pl -type=ncbi -file=ids.txt -column=hgnc_id -column=symbol

Options:
  -help            Brief help message.
  -man             Full documentation.
  -type            Gene ID type within the file.
  -file            File name containing the list of gene IDs.
  -column          This argument can be used multiple times. Will
                   retrieve the columns specified from the gene report.

DESCRIPTION

A perl script which will return tab separated tabular data containing HGNC gene information for each gene ID specified in the user provided file. The script utilises the HGNC REST service and allows the user to retrieve any data that is displayed within our gene symbol reports.

OPTIONS

-help

Print a brief help message and exits.

-man

Prints the manual page and exits.

-type

The type of gene IDs found within the provided file. Type can be one of the following:

ncbi               for NCBI gene IDs eg. 673
hgnc               for HGNC gene IDs eg. HGNC:1097
ensembl            for ensembl gene IDs eg. ENSG00000157764
symbol             for HGNC approved symbol eg. TP53

-file

The path of the txt file that contains a list of gene IDs of the type seen above

-column

Use this flag for each column you want to appear within the output. Columns will be tab separated. For a list of columns that you can use please refer to either our REST help page or using the info REST service command and use any columns under "storedFields".

REQUIREMENTS

This will only work for macs and linux machines. Git must be installed.

This code has been tested on MacOSX 12.4 using both perl 5.16.0 & 5.30.3.

Mac users

If you haven't install git or xcode and you initiate a git clone, your mac may ask you to install xcode. Please install this app and try to git clone once again.

INSTALL

To install this command line tool, clone this project into your directory of choice:

git clone https://github.com/HGNC/get-gene-info.git

Once cloned you then need to change into the projects directory and run the install script:

cd ./get-gene-info && ./install.sh

The install script will download all the required modules needed for the script and will test the script. Once successfully install you may use the script as described above.

Install video