wbazant

“All right," said Susan. "I'm not stupid. You're saying humans need... fantasies to make life bearable."

REALLY? AS IF IT WAS SOME KIND OF PINK PILL? NO. HUMANS NEED FANTASY TO BE HUMAN. TO BE THE PLACE WHERE THE FALLING ANGEL MEETS THE RISING APE.

"Tooth fairies? Hogfathers? Little—"

YES. AS PRACTICE. YOU HAVE TO START OUT LEARNING TO BELIEVE THE LITTLE LIES.

"So we can believe the big ones?"

wbazant

use Atlas::AtlasAdmin;
use Atlas::Common qw(
	connect_atlas
	create_atlas_site_config
	get_atlas_contrast_details
	get_log_file_header
	get_log_file_name
);
use Atlas::AtlasConfig::Reader qw(

wbazant

#count assay groups per experiment - $ATLAS_FTP/experiments
for e in $(ls /ebi/ftp/pub/databases/microarray/data/atlas/experiments | grep E-); do grep -P '<assay' $e/$e-configuration.xml | grep -v assay_group | wc -l | awk -v "EXP=$e" '{print EXP "\t" $1}'; done | tee /var/tmp/assay-groups-per-exp-prod.txt

#count assay groups per experiment - $ATLAS_EXPS

for e in $(ls /nfs/public/ro/fg/atlas/experiments | grep E-); do grep -P '<assay' $e/$e-configuration.xml | grep -v assay_group | wc -l | awk -v "EXP=$e" '{print EXP "\t" $1}'; done | tee /var/tmp/assay-groups-per-exp.txt

#assay groups in last release
cat /var/tmp/assay-groups-per-exp-prod.txt | cut -f 2 -d $'\t' | paste -sd+ - | bc
#82485

wbazant

commit c9a0dd8fb02fae9e4b7e032eb849c89f4964329b
Author: Alfonso Muñoz-Pomer <[email protected]>
Date:   Fri May 19 00:56:18 2017 +0100

    Production bundles - Final release version
    
commit 10d65001c2a9c65964495ccfb996b71081697428
Author: Alfonso Muñoz-Pomer <[email protected]>
Date:   Fri May 19 00:41:48 2017 +0100

wbazant

SQL> SELECT experiment_organism.organism, experiment.type, count(experiment_organism.organism) as c FROM experiment LEFT OUTER JOIN  EXPERIMENT_ORGANISM on EXPERIMENT_ORGANISM.EXPERIMENT=EXPERIMENT.ACCESSION WHERE private = 'F' group by experiment.type, experiment_organism.organism order by -c;

ORGANISM
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
TYPE
--------------------------------------------------
         C
----------
Homo sapiens
MICROARRAY_1COLOUR_MRNA_DIFFERENTIAL                      929

wbazant

wbazant-ml:open_targets wbazant$ jq -c 'select(.evidence.confidence_level=="high") | select (.target.activity=="http://identifiers.org/cttv.activity/unknown") | .unique_association_fields.study_id  ' /var/tmp/cttv010-10-05-2017.json | sort -u | grep  -oe 'E-[[:upper:]]*-[[:digit:]]*' | tee /var/tmp/unknown-activity-high-confidence.txt
E-GEOD-1420
E-GEOD-19187
E-GEOD-20189
E-GEOD-21899
E-GEOD-2461
E-GEOD-31138
E-GEOD-32175
E-GEOD-3325
E-GEOD-36076

wbazant

# monthly stats - experiment page views
wbazant-ml:atlas wbazant$ cat /var/tmp/access-E-MTAB-4840.txt | cut -f 1 -d : | xargs -n1 -I {} date -j -f "%d/%b/%Y" {} '+%Y-%m' | sort | uniq -c
   2 2016-11
 160 2016-12
 166 2017-01
 284 2017-02
 564 2017-03
 853 2017-04
 437 2017-05
 215 2017-06

wbazant

wbazant

{
  "type": "object",
  "properties": {
    "okay_property": {}
  },
  "additionalProperties": false
}

wbazant

{
    "type": "object",
    "id": "#madness",
    "properties": {
         "method": {
            "$ref":"https://gist.githubusercontent.com/wbazant/2cd464750322f065d329c4f75b1fb799/raw/59214a2d967242efe7518ce25b0b444511a4f639/method.json"
         }
    },
    "additionalProperties": false
}