line switches.

This program takes the master tables from the production database
and compares it to the corresponding tables on the given servers (by
default, the staging servers).

The program will display any discrepancies on the display
while writing SQL to files in the current directory that will
correct the discrepancies.

Each SQL patch file will have the generic name "fix-DBNAME.sql"
where "DBNAME" is the name of the database, e.g.,
"fix-oryctolagus_cuniculus_otherfeatures_60_3.sql".

A discrepancy is patched by

1)  Insertion into the master table in the production database in the
    case where a new entry has been added to a database without being
    added to the master table.

2)  Insertion into the database table in the case where a new master
    entry is missing in the database.

3)  Updating the database entry in the case where an entry (identified by
    its primary key only) differs in any of its fields.

The SQL patch files may then be used to patch the databases:

  $ mysql -h server -u user -ppass < fix-DBNAME.sql




                    BE SURE TO REVIEW THESE SQL PATCH FILES
                        (along with the program output)

                            WITH YOUR EYE AND BRAIN

                              BEFORE APPLYING THEM

the wrong directory.

# This little script will bootstrap the master tables in the production
# database (and nothing else).  This means copying the relevant tables
# from a known correct database (the "template database") into the
# master_% tables in the production database.
#
# The template database needs to live on the same server as the
# production database.
#
# The otuput of this script is SQL written to standard output.  The SQL
# needs to be run against the MySQL server manually.
#

canonical transcript.

return undef (which is not a good array reference).

Code originally allowed a user to not specify a DBConncetion during construction. This is not the right behaviour and has now been tidied up

calculations, implemented by Steve Searle.

# patch_59_60_c.sql
#
# Title:
#   A patch to fix a couple of inconsistencies in the schema.
#
# Description:
#   QC turned up issues with the signedness of a number of fields in
#   the Ensembl Core schema.  This patch fixes these.  The fields
#   are: karyotype.seq_region_start, karyotype.seq_region_end and
#   seq_region.length (should all be UNSIGNED).

to find.

#
# Title:
#   A patch to fix a couple of inconsistencies in the schema.
#
# Description:
#   A couple of fixes to the schema to do with inconsistencies found
#   during QC.

get_all_DBEntries().  From Michael S.

unneccesarily in add_Attributes().  Transcript attributes do not affect
exon sequences.  Also, the code tried to fiddle with the internals of
the exon object, which is a no-no (especially since those particular
internals did not exist!).

While at it, I changed a few of "$hash->{'key'} = undef" into
"delete($hash->{'key'})".

conditional operator.

In fetch_all_by_Transcript():  Be absolutely sure not to add the
exon_transcript table twice.  Should solve a bug reported by Jan.

In translation_id(): Update for this method.

All from Michael S.

throw() has the correct message (but leave it commented out since it
would stop circular genomes working).

In overlap_size(): Correct documentation.


All from Michael S.

Michael S.

Also, reformat method.