Using fetchChromSizes [1] and selecting *Download the full sequence report*
from the NCBI assembly overview [2] we can generate a mapping from UCSC
chromosome names to accession numbers:

    ./fetchChromSizes hg38 > human.hg38.genome
    for contig in $(cut -f 1 human.hg38.genome | grep 'alt$'); do
        code=$(echo $contig | cut -d _ -f 2 | sed 's/v/./')
        echo -n $contig$'\t'
        grep $code GCF_000001405.26.assembly.txt | cut -f 7
    done > alt_chrom_names.mapping

Generate the JSON dictionary entries:

    >>> import json
    >>> entries = []
    >>> for line in open('alt_chrom_names.mapping'):
    ...     chr, acc = line.strip().split()
    ...     entries.append({'organelle': 'nucleus',
    ...                     'name': chr,
    ...                     'accession': acc})
    ...
    >>> print json.dumps(entries, indent=2)
    [
      {
        "organelle": "nucleus",
        "name": "chr12_KI270837v1_alt",
        "accession": "NT_187588.1"
      },
      {
        "organelle": "nucleus",
        "name": "chr13_KI270842v1_alt",
        "accession": "NT_187596.1"
      },
      ...
    ]

[1] http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes
[2] ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.26.assembly.txt

See http://pytest.org/

Based on comments by Jeroen in issue #14.

See http://semver.org/

Because we don't know how to name them anyway. We also ignore genes
without any transcripts.

The LRG model allows for more than one CDS per transcript (and each CDS
can be coupled with more than one transcript). The Mutalyzer gene model
does not allow that.

Previously, multiple CDSs per transcript where treated incorrectly (I
think), so now we just ignore any CDS except the first per transcript.

Unfortunately, it is a bit more involved to give good warnings for this,
so that is not implemented.

The web interface for the syntax checker previously automatically
removed comma characters from the description before parsing it. This
is not a good idea, mainly because comma characters are actually
allowed by the nomenclature (to distinguish different molecules on
RNA level).

Furthermore, this behaviour was a special case for the syntax checker
website interface and not present in either the batch or webservice
interfaces, nor in the name checker or any other interface.

This is quite a large commit, touching many things related to developer
documentation. It is all focussed on getting as much of this as possible
into the new Sphinx-based documentation.

Some highlights:

- Start Sphinx-based developer documentation, including fairly complete
  instructions for installation and configuration.
- Remove epydoc API docs.
- Rework some docstrings to conform to reStructuredText, so they can be
  used in the API docs generated by Sphinx.
- Move all of the top-level text files to reStructuredText so they can
  linked from the Sphinx-based docs and for consistency.
- Remove many obsolete things from the extras/ directory, including old
  installation scripts and migrations.

Many of the installation related documentation and scripts are removed
or adapted in light of the new automated deployment using Ansible.