See http://pytest.org/

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.

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

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.

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@639 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@573 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@572 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@570 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@567 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@558 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

This fixes Trac bug #95.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@524 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Until now, the name checker form used POST requests. As a special case for
linking from LOVD, GET requests were handled by showing results without the
full interface (header, menu, etc). Ordinary linking was done to a separate
checkForward location which then set a cookie with the variant name and a
redirect to the name checker results. This was all very hackish and somewhat
broken (see Track issue #94).

This commit refactors the name checker to use GET requests, so ordinary
bookmarking of result pages is possible. All old entrypoints are handled with
a redirect for backwards compatibility.

Worth mentioning is that variant descriptions in the name checker are now
limited in length by the maximum query string length. However, this maximum
is several thousand characters with Internet Explorer having the lowest
maximum of just over 2000. Longer descriptions are not practically checked
with the name checker web interface anyway, so this should not be a problem.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@521 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@502 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

During import of the NCBI transcript mappings, CDS start or stop positions
were not picked up for some transcripts (where these are on exon boundaries).

Bug reported by S Venkata Suresh Kumar.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@490 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@420 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

The old way of using the configuration file was by instantiating a Config
object which read the file. This instance was passed to every function and
object that might need it.

The new way is by simply calling config.get('name') to get the configuration
value for 'name'. This lazily reads the configuration file and the contents
are cached for future calls.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/implicit-config-branch@408 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Convert the 'hg18.map' and 'hg19.map' tables are to 'hg18.Mapping' and
'hg19.Mapping'. These tables are now updated with mapping info from the
NCBI instead of the UCSC.

Also added database and configuration file migration scripts.

extras/config.example:
- Remove configuration values for UCSC updates.

extras/post-install.sh:
mutalyzer/Mapper.py:
mutalyzer/Db.py:
- Use 'Mapping' table instead of 'map' table.

extras/cron.d/mutalyzer-mapping-update:
mutalyzer/Mapper.py:
mutalyzer/Db.py:
- Get mapping updates from the NCBI.

extras/migrations:
extras/post-upgrade.sh:
- Automated migration scripts.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@342 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@338 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1