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

[Michael Yourshaw]

I don’t think that would work well as a general solution. What about implementing a specific hash key to designate text that would be output before the column info, such as “$$PRELUDE”? The value associated with the $$PRELUDE key would be put into the header before the column info. If the value were multiline (\n separated” VEP could nicely add the “##” before each line, so VEP maintains control over how the header is formatted.


This is obviously not a big deal, but would be a convenience.

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

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On Apr 5, 2012, at 01:30, Graham Ritchie wrote:

> 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.
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
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>> 
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> 
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