dbolser

SELECT
  s.name
FROM
  seq_region s
INNER JOIN
  seq_region_attrib USING (seq_region_id)
INNER JOIN
  coord_system c USING (coord_system_id)
LEFT JOIN
  assembly ON seq_region_id = asm_seq_region_id

dbolser

ensrw@mysql-eg-staging-2.ebi.ac.uk:4275 (oryza_sativa_core_22_75_7)
> SELECT COUNT(*) FROM exon_transcript;
+----------+
| COUNT(*) |
+----------+
|   248445 |
+----------+
1 row in set (0.00 sec)

dbolser

> SELECT COUNT(*), COUNT(DISTINCT exon_id), COUNT(DISTINCT transcript_id) FROM exon_transcript;
+----------+-------------------------+-------------------------------+
| COUNT(*) | COUNT(DISTINCT exon_id) | COUNT(DISTINCT transcript_id) |
+----------+-------------------------+-------------------------------+
|   248445 |                  248445 |                        248445 |
+----------+-------------------------+-------------------------------+
1 row in set (0.00 sec)


> SELECT COUNT(*), SUM(exon_id is null), COUNT(DISTINCT exon_id), COUNT(DISTINCT transcript_id) FROM exon_transcript;

dbolser

DROP TABLE IF EXISTS test_et;
CREATE TABLE         test_et (
  exon_id       int unsigned NOT NULL,
  transcript_id int unsigned NOT NULL,
  rank          int          NOT NULL,
  ##
  PRIMARY KEY    (exon_id, transcript_id, rank)#,
  #KEY exon       (exon_id),
  #KEY transcript (         transcript_id)
);

dbolser

for module in \
    ensembl \
    ensembl-compara \
    ensembl-funcgen \
    ensembl-rest \
    ensembl-tools \
    ensembl-variation
do
    if [ ! -d "$module" ]; then
        echo "Checking out $module ($branch)"

dbolser

#!  perl

use strict;
use warnings;

die "pass an intron-style GFF for me to calcualte exons over\n"
  unless @ARGV;

## Tracking variables
my $prev_type = 'dumped';

dbolser

<?php
/**
 * @file
 * Apache Solr external index module - example module for using external data.
 */

/**
 * implements hook_apachesolr_query_alter().
 */
function apachesolr_external_index_apachesolr_query_alter(DrupalSolrQueryInterface $query) {

dbolser

#!perl

use strict;
use warnings;

## Easy manipulation of sets of integers (arbitrary intervals)
use Set::IntRange;

## Create two sets to play with
my $set_len = 1000000000;

dbolser

diff --git a/modules/Bio/EnsEMBL/EGPipeline/Xref/UniProtLoader.pm b/modules/Bio/EnsEMBL/EGPipeline/Xref/UniProtLoader.pm
index ceec266..739fd31 100644
--- a/modules/Bio/EnsEMBL/EGPipeline/Xref/UniProtLoader.pm
+++ b/modules/Bio/EnsEMBL/EGPipeline/Xref/UniProtLoader.pm
@@ -196,6 +196,10 @@ sub add_uniprot_xrefs {
 
 sub store_uniprot_xrefs {
   my ( $self, $ddba, $tid, $uniprots, $gene_id, $gene_attribs ) = @_;
+
+  my $n = 0;

dbolser

21:13 < dbolser_> On another issue... I'm usign LWP::Simple to grab this: 
                  https://letstalkbitcoin.com/api/v1/forum/threads, which is 
                  "Content-Type:application/json", however, when I decode_json 
                  (using JSON), I get the error: malformed JSON string, neither 
                  array, object, number, string or atom, at character offset 0 
                  (before "\x{ef}\x{bb}\x{bf}{"...") at ./get_and_load_data.plx 
                  line 24
21:14 < dngor> Maybe it's compressed.
21:14 < mauke> no, UTF-8 BOM
21:14 < mauke> a.k.a. malformed JSON