See http://pytest.org/

The name checker supports reverse complement ranges in insertions
and insertions-deletions, for example `3_4ins8_12inv'.

Reverse complement range insertions and insertion-deletions are not
part of the current HGVS nomenclature, but will be proposed.

The name checker supports ranges in insertions and insertion-
deletions, for example `3_4ins8_12`, and compound insertions and
insertion-deletions, for example `3_4ins[ATC;8_12]`.
The inserted sequences are accepted and concatenated before any
further processing, so reported descriptions show only the
concatenated sequences.
The support for ranges is limited to genomic descriptions.

The position converter supports compound insertions and
insertion-deletions, not ranges.

Compound insertions and insertion-deletions are not part of the
current HGVS nomenclature, but will be proposed.

Also, the value for nuclear chromosomes is now `nucleus` instead of
`chromosome` for better alignment with the other value `mitochondrion`.

Note that I did not bother to make an Alembic migration for this, since
we don't have any installations besides my own yet anyway.

This is The Good Stuff. The entire test suite can now be run without
having to setup a database, running the batch checker, any of the web
services or the website. It even passes without an internet connection.
In, like, 30 seconds! Awesome!

This means tests don't randomly fail after some reference sequence
changes on the NCBI server and it doesn't take an entire configured
server with mapping database setup to run the tests. Those are things
of the past! No more frustrations, Mutalyzer is testable!

Going down now...

The mountain screamed three times today
I guess it thought it'd like to play
How much does one have to pay
To fry a peak and melt away
Launching titan's breath on mine
The sweating measure lands on time

And the old man, down by the river
Well he walks up and he walks on down
To the spaceship that's parked at your doorstep
And it's waiting to take you away now

Goin' down now
Goin' down now

Looking for the rate that crowed
He's hooked up down in Mexico
Slap my nerve now give me more
It's my disaster friend, not yours

And the old man, down by the river
Well he walks up and he walks on down
To the spaceship that's parked at your doorstep
And it's waiting to take you away now

And the last one, it's down by the river
Where he gets up and he walks on down
To the spaceship that's parked at your doorstep
And it's waiting to take you away now

It's down by the river, it's always this way now
It's down by the river, it's always this way now

Going down now
Going down now
now, now, now

down, down, down

Now that we ported the database to SQLAlchemy, we remove the obsolete Db
module and all references to it.

The Redis client automatically falls back to a mock Redis server if no
Redis server is configured. Therefore, a Redis server is not needed to
run Mutalyzer. You'll just not get any aggregate stat counts over
different runs.

This introduces a proper notion of genome assemblies. Transcript
mappings for alle genome assemblies are in the same database, which
is better for maintenance. Updating transcript mappings is also
simplified a lot, especially from NCBI mapview files where we now
require a preprocessing sort on the input file.

Overall, this port touches a lot of Mutalyzer code, so beware.

This involves making the SQLAlchemy session reconfigurable at run-time,
which is done automatically on updating the Mutalyzer configuration using
configuration update callbacks.

Port the entire batch job infrastructure, including scheduler, to use
the SQLAlchemy ORM instead of the old Db module.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@746 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@743 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@664 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@663 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/lrg-schema-update@654 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@639 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Support genomic references in the mapping database. At the moment, this is
only tested with mtDNA genes, but should in clear the way for NG_ mappings
as well.
Mappings for mtDNA genes can be added to the database using the command line
tool mutalyzer-mapping-import.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@635 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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