[ensembl-dev] VEP dbNSFP plugin

[Will McLaren]

Thanks Michael, I've updated the plugin.

Will


On 14 November 2013 21:35, Michael Yourshaw <myourshaw at ucla.edu> wrote:

> I’m not sure this is the right list to bring this up, but the dbNSFP
> plugin can cause a problem on non-windows machines.
>
> The symptom is that if you select the ESP6500_EA_AF column option for
> this plugin, the Extra column in the VEP output will have a CR that might
> be interpreted as a line break immediately after the ESP6500_EA_AF value.
>
> This is because the dbNSFP data file has windows-style (CRLF) newlines
> and ESP6500_EA_AF is the last column in each record.
>
> An easy fix is to add a cleanup line in the dbNSFP plugin:
>     while(<TABIX>) {
> chomp;
> #remove trailing CR on linux platforms
> s/\r$//g;
> my @split = split /\t/;
>
> You might consider having VEP recode any forbidden semicolon, tab, CR, or
> LF (or other?) values that any plugin adds to EXTRA.
>
>
> 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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