[ensembl-dev] Error on using parse_ncbi_gff3.pl

[Daniel Barrell]

Hi David,

Line 1184334 is the last line of the GFF3 file and contains '###'. There
used to be code to ignore lines like these:

+ next if $line =~ /^#/;

When the script moved to use ensembl-io I think it may have lost this
check, however I would expect ensembl-io to handle the '###'. Which species
files worked? I checked on NCBI and other species (e.g. horse) would also
fail in the same way.

Dan






*Daniel Barrell*
Platform Specialist
*eagle*discover Best of Show Winner at Bio-IT World 2016

*Eagle Genomics Ltd*
T: +44 (0)1223 654481
http://www.eaglegenomics.com
Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/

https://youtu.be/rPdgFTo0FZM

On 20 September 2016 at 11:16, Herzig, David <david.herzig at roche.com> wrote:

> Hi Ensembl Users
>
> I have setup the ensembl environment for several species. Everything is ok.
> After that I imported data from NCBI by using the parse_ncbi_gff3.pl
> script. Works fine for almost all species. But for the specie sus scrofa I
> have the following issue:
>
> I downloaded the file from NCBI:
> /ftp.ncbi.nlm.nih.gov/genomes/Sus_scrofa/GFF/ref_Sscrofa10.
> 2_top_level.gff3
>
> I used the parse_ncbi_gff3.pl script to import it.
>
> The process starts successfully but after a while I get the following
> error message and the process stops:
>
> Can't call method "phase" on an undefined value at
> /home/ensembl/release-85/ensembl-pipeline/scripts/refseq_import/
> parse_ncbi_gff3.pl line 882, <__ANONIO__> line 1184334.
>
> Any ideas?
>
> regards,
> David
>
>
> --
>
> David Herzig
> Scientist, pRED Informatics
> Roche Pharma Research and Early Development
>
> Roche Innovation Center Basel
>
> F. Hoffmann-La Roche Ltd
> Grenzacherstrasse 124
> 4070 Basel
> Switzerland
> Phone +41 61 687 31 70
>
> Learn more about pRED Informatics at http://go.roche.com/*pREDi*
> <http://go.roche.com/pREDi>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20160920/81218de7/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: E_Email_Sig.jpg
Type: image/jpeg
Size: 36746 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20160920/81218de7/attachment.jpg>