Add prefix consistency check

[leannehaggerty]

@Ensembl/plantazoa can you please check that this new consistency check works for your stable IDs? If not, I can update so that it only runs on genebuild cores.

Updated Stable ID check to check that all prefixes per features are consistent.

Tested:
changed prefix for one gene from ENSIMR -> ENSXXX, then test fails

 perl $ENSCODE/ensembl-datacheck/scripts/run_datachecks.pl -host mysql-ens-genebuild-prod-6 -port 4532 -user ensro -dbname leanne_gca964332325v1_core_113_1 -dbtype core -n GeneStableID
GeneStableID ..
# Subtest: GeneStableID
    # Subtest: acropora_muricata_gca964332325v1, core, leanne_gca964332325v1_core_113_1, EnsemblMetazoa
        ok 1 - gene table has non-NULL stable IDs
        ok 2 - gene table has unique stable IDs
        ok 3 - transcript table has non-NULL stable IDs
        ok 4 - transcript table has unique stable IDs
        ok 5 - exon table has non-NULL stable IDs
        ok 6 - exon table has unique stable IDs
        ok 7 - translation table has non-NULL stable IDs
        ok 8 - translation table has unique stable IDs
        # Observed base prefixes per table:
        #   exon         : ENSIMR
        #   gene         : ENSIMR, ENSXXX
        #   transcript   : ENSIMR
        #   translation  : ENSIMR
        not ok 9 - Stable ID base prefix is consistent across genes, transcripts, exons and translations

        #   Failed test 'Stable ID base prefix is consistent across genes, transcripts, exons and translations'
        #   at /hps/software/users/ensembl/genebuild/leanne/repositories_tmp/ensembl-datacheck/lib/Bio/EnsEMBL/DataCheck/Checks/GeneStableID.pm line 133.
        1..9
        # Looks like you failed 1 test of 9.
    not ok 1 - acropora_muricata_gca964332325v1, core, leanne_gca964332325v1_core_113_1, EnsemblMetazoa

    #   Failed test 'acropora_muricata_gca964332325v1, core, leanne_gca964332325v1_core_113_1, EnsemblMetazoa'
    #   at /hps/software/users/ensembl/genebuild/leanne/repositories_tmp//ensembl-datacheck/lib/Bio/EnsEMBL/DataCheck/DbCheck.pm line 737.
    1..1
    # Looks like you failed 1 test of 1.
not ok 1 - GeneStableID

#   Failed test 'GeneStableID'
#   at /hps/software/users/ensembl/genebuild/leanne/repositories_tmp//ensembl-datacheck/lib/Bio/EnsEMBL/DataCheck/BaseCheck.pm line 170.
1..1
Failed 1/1 subtests

Test Summary Report
-------------------
GeneStableID (Wstat: 0 Tests: 1 Failed: 1)
  Failed test:  1
Files=1, Tests=1,  4 wallclock secs ( 0.23 usr +  0.03 sys =  0.26 CPU)
Result: FAIL

Info about the new check:
Given a stable_id, we first drop any .version, then we strip trailing digits. From the remaining letters/underscores, if the last character is one of G T E P (the feature-type letter), we remove that one letter to get the base prefix. Examples:

• ENSG00000123456.3 → ENSG00000123456 → remove digits → ENSG → remove feature letter G → ENS
• ENSMUST00000123456 → remove digits → ENSMUST → remove T → ENSMUS
• BRAKERXXXT00001234 → remove digits → BRAKERXXXT → remove T → BRAKER

[EreboPSilva]

Looks good to me.

[vsitnik]

stable_id_prefix_consistency_check should be selected based on 'genebuild.method' metakey

[vsitnik]

Could you condition it with a genebuild.method ?
Like we have it here

ensembl-datacheck/lib/Bio/EnsEMBL/DataCheck/Checks/GeneSymbols.pm

Line 39 in 676250c

SKIP: {

[vsitnik]

Need to check this for metazoa/plants data. Most likely is not true for microbes if translations have the same sequences, as they are using sequence derived hashes as IDs.
Upd. Checked. Seems to be hold.