The module parses MAF formatted files (https://cgwb.nci.nih.gov/FAQ/FAQformat.html#format5).

This is mainly meant to be used through MafIndex.search and
MafIndex.get_spliced methods, which, at this stage, expect lists of
start and end coordinates, where both starts and ends are zero-based
inclusive (0 is the first alignment position). To ask for the alignment
portion corresponding to the first 100 nucleotides of the reference
sequence, you would use MafIndex.get_spliced([0], [99])

As I commented in the pull request discussion
(biopython#504 (comment)):

> I decided to do "zero-based" because MAF format is zero-based. But I
> decided to make the end coordinate inclusive, because it is not very
> intuitive for the human user to have to provide a list of "inclusive"
> start coordinates, but "exclusive" end coordinates when calling
> MafIndex.search and MafIndex.get_spliced.

This commit is based on work by the following contributors (the commits
have been squashed during rebase):

https://github.com/polyatail
https://github.com/peterjc
https://github.com/adamnovak
https://github.com/blaiseli

Also tried to fix style issues (as reported by pylint).

I had renamed MafIterator to maf_iterator to respect style conventions,
but this conflicts with other Bio* conventions.

Reverted inefficient "avoid dots" technique.

- from commit 49e7da7:

    Remove unwanted white space after docstrings (etc)

    $ pydocstyle Bio/ BioSQL/ Tests/ Scripts/ Doc/ --select D202
    ...
    D202: No blank lines allowed after function docstring

- from commit a8cf8c0:

    Avoid ValueError for file not found

    Aim here was to be user friendly, but a file-system relevant
    exception is probably better for error handling.

Trying to fix biopython#1083

…nto alignio-maf

…nto alignio-maf

…nto alignio-maf