Uncertain stop codon in protein descriptions (fs and ext)

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

Dog assembly

Release 2.0.9

Usability improvements in reading DNA for description extractor

Don't trust encoding auto-detection when decoding

Use chardet instead of cchardet

Issue #50 showed a problem in our file encoding detection, caused
by our cut-off for the confidence as reported by the cchardet [1]
library:

    >>> import cchardet
    >>> s = u'NM_000052.4:c.2407\u20132A>G'
    >>> b = s.encode('WINDOWS-1252')
    >>> cchardet.detect(b)
    {'confidence': 0.5, 'encoding': u'WINDOWS-1252'}

We require a confidence stictly greater than 0.5 and default to
UTF8 otherwise.

If, however, we try the same thing using the chardet [2] library,
we get a higher confidence for the same string:

    >>> import chardet
    >>> chardet.detect(b)
    {'confidence': 0.73, 'encoding': 'windows-1252'}

So the two obvious ways to solve this are:

1. Lower the confidence threshold.
2. Use chardet instead of cchardet.

We implement the second solution here, since it also removes a C
library dependency and we are not worried by performance.

Of course the detected encoding remains a guess which can still
be wrong!

[1] https://github.com/PyYoshi/cChardet
[2] https://github.com/chardet/chardet

Fixes #50

Add NG example to name checker website form

Configurable maximum input length for description extractor

Adds a `EXTRACTOR_MAX_INPUT_LENGTH` configuration setting, defaulting
to 50 Kbp.

Show filename of uploaded file in description extractor

Release 2.0.8

Fix broken example input links

Fixes #43

Track stats for description extractor

Description extractor web interface

This is hopefully a temporary measure. At the moment we cannot accurately
predict the running time of the extractor, so we have to aggressively
limit the input based on the worst-case expectation.

As a worst-case scenario, we currently use random input sequences, where
length 1000bp yields about 500ms of running time.

In the future we hope to either:

1. Predict the running time and abort if needed.
2. Keep track of the running time and abort if needed.
3. Run the extractor in a task scheduler with a running time limit.

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.