Template Comparison

We have written a script that runs queries against the templates publicly available in a mine or a pair of mines. The purpose of these scripts is to:

• Test that all templates run.
• In the case of multiple mines, check that updates haven't radically changed the results.

The script presents their results on standard out, with the option to have them emailed upon completion of the comparison. To have results emailed out, you should have set up and installed sendmail on the machine running the comparison.

The script is located here: https://github.com/intermine/intermine-release-scripts/blob/master/compare_templates_for_releases.py

Python Script

Dependencies

This script will run on cPython 2.5-2.7, pypy and jython. It requires the installation of the intermine client module, which can be installed from PyPi with the following command:

$ sudo easy_install intermine

Invocation

The script can be invoked most simply against a single mine as follows:

$ python compare_templates_for_releases.py www.flymine.org/flymine

To have results emailed, add your email address:

$ python compare_templates_for_releases.py www.flymine.org/flymine you@your.host.org

Optionally set a ''from'' address:

$ python compare_templates_for_releases.py www.flymine.org/flymine you@your.host.org noreply@blackhole.net

Comparing against two mines is same as above, except you simply need to add a second service location:

python compare_templates_for_releases.py www.flymine.org/flymine beta.flymine.org/beta you@your.host.org

Results

The resulting email will look like this:

-----------------------------------In Both: Diff >= 10%

BDGP_Gene release-beta: 260, release-28.0: 62, diff: 76%

ChromLocation_CRMOverlappingTFBindingsite release-beta: 42, release-28.0: 213, diff: 80%

----------------------------------------------------------------------

-----------------------------------Only in 28.0:

ChromosomeLocation_Tiffin 8

Disease_GeneOrthologue 363

ESTclone_LocationOverlappingGeneOrthologue_new 93

ESTclone_LocationOverlappingGeneStructure 4

Gene_Inparalogue 11

Gene_Tiffin 156

Probe_Gene 1

TiffinBSmotif_expressionTerm 49

TiffinBSmotif_genes 1356

TiffinBSmotif_locations 23

----------------------------------------------------------------------

-----------------------------------Only in beta:

Amplicon_RNAiResults 39

Gene_AdjacentGene_FlyAtlas_downstream 0

Gene_OverlapppingGenes 1

Genes_Publications 126002

Organism_interologs 278

--------------------------------------------------In Both: Diff < 10%

All_Genes_In_Organism_To_Publications release-beta: 126002, release-28.0: 121503, diff: 4%

AlleleClass_Allele release-beta: 2132, release-28.0: 2117, diff: 1%

1. '''In Both: Diff >= 10%''' - templates run in both mines and result counts returned were very different.
2. '''Only in''' - template was found in one mine and not the other.
3. '''In Both: Diff < 10%''' - template run in both mines and results returned were different. It's probably safe to assume these are okay.