With this change the genbank parser no longer discards incomplete genes
directly but keeps them as long as they have complete features
annotated.

For example, the PIK3R2 gene is annotated on NC_000019.9 (or a slice) as
4973..>22328 with two RNA entries. One of these, however, is complete so
it would be a shame to discard the entire gene.

This genbank file is incomplete and incorrect anyway, but this was
not the mistake we want to test.

Partial fix for https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/188

In case of an alternative start codon, the variant CDS was not
translated to a protein starting with M. This caused the protein
description machinery to conclude a variant affecting the start
codon, hence reporting `p.?`.

We fix this by always translating the start codon to M (except
when the variant actually affects it).

Example: `NM_024426.4:c.1107A>G` (a synomymous mutation) should
yield `NM_024426.4(WT1_i001):p.(=)`, not `p.?`. The start codon
for that protein is `CTG`.

When a variant results in a frame shift or extension and we don't
see a new stop codon in the RNA, the protein description should use
the notation for an uncertain stop codon, e.g., `p.(Gln730Profs*?)`
instead of `p.(Gln730Profs*96)` where 96 is just the last codon in
our transcript [1].

To detect this, we now use `to_stop=False` in our `.translate()`
calls, since that will explicitely return `*` characters for stop
codons.

We also slightly fix the coloring of changes in the protein sequence
where previously changed stop codon characters where not included.

[1] http://www.hgvs.org/mutnomen/FAQ.html#nostop

Jeroen F.J. Laros authored 9 years ago and Vermaat committed 9 years ago

We can now compare two sequences by supplying their sequence strings,
accession numbers, or uploaded file.

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

- Added error recovery to batch daemon.
- Added example init script for batch daemon.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@244 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1