konradjk/loftee

GERP bigwig file location not concatenated properly

Opened this issue · 4 comments

I'm getting an error:

WARNING: Plugin 'LoF' went wrong: /home/dgealow/.vep/Pluginsgerp_conservation_scores.homo_sapiens.GRCh38.bw does not exist at /home/dgealow/.vep/Plugins/gerp_dist.pl line 72.

Note that it seems to be concatenating the slash-less filepath of the plugin directory I provided with the default expected filename, without a slash in-between. This issue seems to stem from:

loftee/LoF.pm

Line 130 in a46b502

$self->{gerp_bigwig} = $self->{loftee_path} . 'gerp_conservation_scores.homo_sapiens.GRCh38.bw' if !defined($self->{gerp_bigwig});

which I'm guessing should instead use catdir like the other path concatenations, something like this probably:

$self->{gerp_bigwig} = catdir($self->{loftee_path}, 'gerp_conservation_scores.homo_sapiens.GRCh38.bw') if !defined($self->{gerp_bigwig});

Have you solved this problem? I got the same error when using the GRCh37 version, but it worked fine in the GRCh38 version.
Alternatively, could the LoF v1.0.4 be used directly for b37 vcf?

The master branch works fine for b37 vcf, while the latest version of LoF seems to not support GRCh37. This error will disappear if I use the correct version. What do you think?

dvg-p4 commented

@jxcao98 This was a while ago, but I think I was able to just provide the loftee path with a trailing slash as a workaround:

vep --plugin LoF,loftee_path:/home/dgealow/.vep/Plugins/,[...]

Thank you for your reply!