[ensembl-dev] VEP plugin-generated non-column header info

[Graham Ritchie]

Hi Michael,

One simple way to add arbitrary text to the header would be to just return the text you want to include as a key with the empty string as a value in the hash returned from the get_header_info method in your plugin, e.g.:

sub get_header_info {
    return {
        'Human Protein Atlas expression profile data' => '',
        'HPA_ovary_follicle_cells' => "Expression profile for protein in human ovary follicle cells based on immunohistochemisty",
	'HPA_breast_glandular_cells' => "Expression profile for protein in human breast glandular cells based on immunohistochemisty",
    };
}

Having a key in this hash does not require there to be a corresponding column. However, because the entries are returned in a hash, currently lines will be added to the header in an arbitrary order, so the code above will produce the header:

## HPA_breast_glandular_cells   : Expression profile for protein in human breast glandular cells based on immunohistochemisty
## Human Protein Atlas expression profile data  : 
## HPA_ovary_follicle_cells : Expression profile for protein in human ovary follicle cells based on immunohistochemisty

It would be straightforward to sort the keys of this hash to fix the order, but then you'd have to include extra text to ensure this (e.g. prefixing each key with a number). Do you think this would be useful?

Cheers,

Graham


On 5 Apr 2012, at 09:02, Will McLaren wrote:

> Hi Michael,
> 
> Unfortunately no, the headers are added by the main VEP code before
> any of the plugin-specific code is run.
> 
> You could easily add this with a simple perl one liner or awk though?
> 
> Cheers
> 
> Will
> 
> On 5 April 2012 02:27, Michael Yourshaw <myourshaw at ucla.edu> wrote:
>> Does VEP support a mechanism whereby a plugin can add ## comments to the
>> output header without causing the creation of a column?
>> 
>> For example, I might want the header to contain an introductory line,
>> followed by two annotation column definitions:
>> 
>> ## Human Protein Atlas expression profile data:
>> ## HPA_ovary_follicle_cells     : Expression profile for protein in human
>> ovary follicle cells based on immunohistochemisty
>> ## HPA_breast_glandular_cells   : Expression profile for protein in human
>> breast glandular cells based on immunohistochemisty
>> 
>> 
>> 
>> ॐ
>> 
>> Michael Yourshaw
>> 
>> UCLA Geffen School of Medicine
>> Department of Human Genetics, Nelson Lab
>> 695 Charles E Young Drive S
>> Gonda 5554
>> 
>> Los Angeles CA 90095-8348 USA
>> 
>> myourshaw at ucla.edu
>> 
>> 970.691.8299
>> 
>> This message is intended only for the use of the addressee and may contain
>> information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY
>> WORK PRODUCT. If you are not the intended recipient, you are hereby notified
>> that any dissemination of this communication is strictly prohibited. If you
>> have received this communication in error, please erase all copies of the
>> message and its attachments and notify us immediately. Thank you.
>> 
>> 
>> 
>> 
>> 
>> 
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> List admin (including subscribe/unsubscribe):
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/