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java version "1.7.0_201" | |
OpenJDK Runtime Environment (IcedTea 2.6.17) (7u211-2.6.17-0ubuntu0.1) | |
OpenJDK 64-Bit Server VM (build 24.201-b00, mixed mode) |
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EXPLAIN SELECT COUNT(*) FROM tmp_sample_genotype_single_bp; | |
+----+-------------+-------+------+---------------+------+---------+------+------+------------------------------+ | |
| id | select_type | table | type | possible_keys | key | key_len | ref | rows | Extra | | |
+----+-------------+-------+------+---------------+------+---------+------+------+------------------------------+ | |
| 1 | SIMPLE | NULL | NULL | NULL | NULL | NULL | NULL | NULL | Select tables optimized away | | |
+----+-------------+-------+------+---------------+------+---------+------+------+------------------------------+ | |
1 row in set (0.00 sec) | |
EXPLAIN SELECT COUNT(DISTINCT variation_id) FROM tmp_sample_genotype_single_bp; | |
+----+-------------+-------------------------------+-------+---------------+---------------+---------+------+----------+--------------------------+ |
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2018-10-17 10:46:07,108 INFO - Retrieving results for job 117894 | |
2018-10-17 10:46:07,135 INFO - Retrieving results for job 118472 | |
2018-10-17 10:46:07,157 INFO - Retrieving results for job 139103 | |
2018-10-17 10:46:07,181 INFO - Retrieving results for job 139991 | |
2018-10-17 10:46:07,204 INFO - Retrieving results for job 140201 | |
2018-10-17 10:46:07,251 INFO - Retrieving results for job 158129 | |
2018-10-17 10:46:07,273 INFO - Retrieving results for job 158264 | |
2018-10-17 10:46:07,296 INFO - Retrieving results for job 169452 | |
2018-10-17 10:46:07,317 INFO - Retrieving results for job 170266 | |
2018-10-17 10:46:07,339 INFO - Found tag one_off_test-20181017101930 for job: 171589 |
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<?xml version="1.0"?> | |
<!-- | |
Targets for checking out dependencies for the healthchecks. | |
Use | |
ant clean | |
to delete the directory with the checkouts. |
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<?xml version="1.0"?> | |
<!-- | |
Targets for checking out dependencies for the healthchecks. | |
Use | |
ant clean | |
to delete the directory with the checkouts. |
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SET @i=1; | |
SET @l=10000000; | |
SELECT * FROM seq_region INNER JOIN (SELECT @i, @i:=@i+@l AS x) AS der | |
ON length < @i | |
WHERE seq_region_id = 196420; | |
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## Get BioMart | |
git clone https://github.com/biomart/biomart-perl.git | |
## Get ready | |
cd biomart-perl/scripts | |
## Get Sharon's script from here: |
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# An example script demonstrating the use of BioMart API. | |
# This perl API representation is only available for configuration versions >= 0.5 | |
use strict; | |
use BioMart::Initializer; | |
use BioMart::Query; | |
use BioMart::QueryRunner; | |
my $confFile = "../conf/martURLLocation.xml"; |
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source /homes/dbolser/EG_Places/Devel/lib/libensembl-94/setup.sh | |
release=41 | |
# $ENSEMBL_ROOT_DIR/ensembl-production/scripts/process_division.sh \ | |
# EPl mysql-pan-prod ensembl_production $release \ | |
# > db_to_copy.txt | |
ENDPOINT=http://eg-prod-01.ebi.ac.uk:7000/hc/ |
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from runstats import Statistics | |
stats = Statistics() | |
i=0 | |
with open("dupes_default_run_scores.tsv") as tsv: | |
next(tsv) | |
for line in tsv: | |
i=i+1 | |
line=line.rstrip() |
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