wbazant’s gists

wbazant / E-MTAB-4840-access-stats.txt

Last active August 3, 2017 14:38

	# 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 / unknown-activity-high-confidence.txt

Created June 13, 2017 11:30

	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 / atlas-select-stats.sql

Created May 24, 2017 10:11

	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 / atlas_releases.txt

Created May 19, 2017 10:00

	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 / atlas-count-assays-in-experiments.sh

Created May 15, 2017 16:45

Atlas numbers

	#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 / debug-pmids.pl

Created May 9, 2017 11:16


	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 / hogfather.txt

Last active February 8, 2017 18:13

	“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 / does_go_replacement_happen.sh

Created February 7, 2017 12:28

	cd ~/dev/atlas-annotations
	# modify the annsrcs to be (much) smaller
	# test environment
	source util/create_test_env.sh /var/tmp/will-it-go

	# use the whole file from prod
	scp ebi-cli:/nfs/production3/ma/home/atlas3-production/bioentity_properties/go/go.alternativeID2CanonicalID.tsv /var/tmp/will-it-go/bioentity_properties/go/go.alternativeID2CanonicalID.tsv

	# get some properties populated in test environment
	export JAVA_OPTS=-Xmx3000M

wbazant / E-GEOD-49608-analysis.tsv

Created February 2, 2017 15:17

We can make this file beautiful and searchable if this error is corrected: No tabs found in this TSV file in line 0.

	Gene ID Gene Name g1_g2.p-value g1_g2.log2foldchange g1_g3.p-value g1_g3.log2foldchange g1_g4.p-value g1_g4.log2foldchange g5_g6.p-value g5_g6.log2foldchange g5_g7.p-value g5_g7.log2foldchange g5_g8.p-value g5_g8.log2foldchange
	ENSG00000000003 TSPAN6 0.00455588947600315 -0.2 1.47389153905488e-05 0.3 5.25735911012297e-74 1.1 0.137744420192993 -0.2 0.0192978221738748 -0.2 1.69287277016467e-07 0.6
	ENSG00000000005 TNMD NA 0 NA 0.2 NA 0.3 NA 0 NA -0.1 NA 0
	ENSG00000124635 HIST1H2BJ 2.062881127556e-210 -1.2 0 -1.5 0 -2.6 2.46220174669173e-223 -1.5 0 -1.5 0 -2.7

wbazant / analytics index build log

Created January 31, 2017 17:50

--- Analytics index build started Tue Jan 31 10:01:04 GMT 2017 ---

Experiments to index: [E-MTAB-2770, E-MTAB-2706, E-MTAB-4840, E-GEOD-48433, E-GEOD-26284, E-MTAB-4342, E-GEOD-18858, E-MTAB-2512, E-MTAB-3579, E-MTAB-4404, E-MTAB-5214, E-MTAB-2919, E-MTAB-76, E-GEOD-53960, E-GEOD-36272, E-MTAB-4045, E-MTAB-1354, E-GEOD-16837, E-GEOD-49284, E-MTAB-4395, E-MTAB-4484, E-MTAB-4222, E-MTAB-3838, E-MTAB-2836, E-MTAB-1729, E-MTAB-3358, E-MTAB-3827, E-GEOD-60424, E-GEOD-53197, E-GEOD-18344, E-MTAB-5140, E-TABM-234, E-MTAB-4270, E-MTAB-1027, E-GEOD-66354, E-GEOD-16879, E-ERAD-401, E-GEOD-18791, E-TABM-142, E-MTAB-4444, E-MTAB-3871, E-GEOD-3307, E-MTAB-2801, E-MTAB-2812, E-GEOD-41678, E-MTAB-2137, E-GEOD-30495, E-GEOD-62673, E-GEOD-15129, E-GEOD-33643, E-GEOD-38351, E-GEOD-63252, E-GEOD-25250, E-MTAB-513, E-GEOD-16992, E-GEOD-63362, E-GEOD-45757, E-JJRD-1, E-GEOD-37940, E-GEOD-38023, E-TABM-1216, E-TABM-1205, E-MTAB-4260, E-TABM-82, E-GEOD-58603, E-MTAB-4289, E-GEOD-49050, E-GEOD-40844, E-MTAB-4308, E-GEOD-13637, E-GE

Wojtek Bażant wbazant