dbolser-ebi

  feature/rna_features
  feature/synteny_stats
  feature/uniprot_goa_loader
  hotfix/blast_filter_hits
* master
  origin/feature/rna_features
  remotes/github/feature/bacteria_uniprot
  remotes/github/feature/dnaseq_align
  remotes/github/feature/dnaseq_align_optimizations
  remotes/github/feature/load_gff3_batch

dbolser-ebi

show create table variation_feature;
+-------------------+----------------+
| Table | Create Table |
|-------------------+----------------|
| variation_feature | CREATE TABLE variation_feature (
variation_feature_id int(10) unsigned NOT NULL AUTO_INCREMENT,
seq_region_id int(10) unsigned NOT NULL,
seq_region_start int(11) NOT NULL,
seq_region_end int(11) NOT NULL,

dbolser-ebi

> desc variation_feature;
...
| consequence_types     | set('intergenic_variant','splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation','feature_elongation','feature_truncation','regulatory_region_variant','TF_binding_site_variant','protein_altering_variant') |

dbolser-ebi

[dbolser@ebi-cli-002 ~]$ pip freeze
You are using pip version 7.1.0, however version 9.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
-ipap11helper==0.1
Babel==0.9.6
backports.ssl-match-hostname==3.4.0.2
Beaker==1.5.4
biopython==1.66
Bottleneck==0.7.0
Brlapi==0.6.0

dbolser-ebi

#!/usr/bin/env perl

use v5.14;
use strict;

use autodie;

use Bio::EnsEMBL::Registry;

Bio::EnsEMBL::Registry->load_registry_from_db(

dbolser-ebi

while read -r md5; do
    echo $md5
    HEAD -d www.ebi.ac.uk/ena/cram/md5/$md5
    if [ $? -eq 1 ]; then
        echo $md5
        break
    fi
done <  ERR392069.cram.header.md5 

dbolser-ebi

1) Go to http://www.ebi.ac.uk/ena/data/view/AEWC00000000 and see 'WGS Sequence Set: AEWC01000000 ...', which is right.
2) https://www.ebi.ac.uk/seqdb/confluence/dashboard.action and notice a cookie called JSESSIONID with path '/seqdb/confluence/'.
3) Go back to the ENA page and delete the cookie called JSESSIONID with path '/ena/data'.
4) Reload the ENA page and notice 'No results found for:   AEWC00000000', which is wrong.
5) Delete the JSESSIONID with path '/seqdb/confluence/' (from the confluence page).
6) Reload the ENA page and notice 'WGS Sequence Set: AEWC01000000...' again.
7) Freak out.

dbolser-ebi

The Chromium Authors
Copyright 2016 The Chromium Authors. All rights reserved.
Chromium	51.0.2704.79 (Developer Build) Built on Ubuntu 14.04, running on LinuxMint 17.2 (64-bit)
Revision	0a967bea2f0b592106657f0af87985ec6b6fe44d
OS	Linux 
Blink	537.36 (@0a967bea2f0b592106657f0af87985ec6b6fe44d)
JavaScript	V8 5.1.281.57
Flash	11.2.999.999
User Agent	Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu Chromium/51.0.2704.79 Chrome/51.0.2704.79 Safari/537.36

dbolser-ebi

### Keybase proof

I hereby claim:

  * I am danbolser on github.
  * I am danbolser (https://keybase.io/danbolser) on keybase.
  * I have a public key whose fingerprint is C6E4 C97A 53DE F36B 560D  8A7B E61C AC74 4189 AE09

To claim this, I am signing this object:

dbolser-ebi

#!/usr/bin/env perl

use 5.14.0;
use warnings;

use autodie qw(:all);

use DBI;

my $dsn =