Zero length sequence ranges aren't allowed if 'strict_bounds=True'

[dhauge]

If a 'Fasta' index is created with 'strict_bounds=True', then attempts to extract 0-length sequences fail. This might be an odd case, but it can happen in limiting cases of algorithms that want to treat the sequence as a standard Python sequence. The following tests demonstrate the error:

class TestZeroLengthSequenceSubRange(TestCase):
    def test_as_raw_zero_length_subsequence(self):
        fasta = Fasta('data/genes.fasta', as_raw=True, strict_bounds=True)
        expect = ''
        result = fasta['gi|557361099|gb|KF435150.1|'][100:100]
        assert result == expect

    def test_zero_length_subsequence(self):
        fasta = Fasta('data/genes.fasta', strict_bounds=True)
        expect = ''
        result = fasta['gi|557361099|gb|KF435150.1|'][100:100]
        assert result.seq == expect

The first raw sequence test fails with

Error
Traceback (most recent call last):
  File "/Users/hauge/dev/tools/pyfaidx/tests/test_feature_sequence_as_raw.py", line 57, in test_zero_length_subsequence
    result = fasta['gi|557361099|gb|KF435150.1|'][100:100]
  File "/Users/hauge/dev/tools/pyfaidx/pyfaidx/__init__.py", line 581, in __getitem__
    return self._fa.get_seq(self.name, start + 1, stop)[::step]
  File "/Users/hauge/dev/tools/pyfaidx/pyfaidx/__init__.py", line 715, in get_seq
    return self.faidx.fetch(name, start, end)
  File "/Users/hauge/dev/tools/pyfaidx/pyfaidx/__init__.py", line 447, in fetch
    seq = self.from_file(name, start, end)
  File "/Users/hauge/dev/tools/pyfaidx/pyfaidx/__init__.py", line 493, in from_file
    "invalid.\n".format(start, end))
pyfaidx.FetchError: Requested coordinates start=101 end=100 are invalid.

If the logic in 'from_file' is fixed to allow a zero-length sequence, the second will still fail when it tries to construct a 'Sequence':

Error
Traceback (most recent call last):
  File "/Users/hauge/dev/tools/pyfaidx/tests/test_feature_sequence_as_raw.py", line 57, in test_zero_length_subsequence
    result = fasta['gi|557361099|gb|KF435150.1|'][100:100]
  File "/Users/hauge/dev/tools/pyfaidx/pyfaidx/__init__.py", line 583, in __getitem__
    return self._fa.get_seq(self.name, start + 1, stop)[::step]
  File "/Users/hauge/dev/tools/pyfaidx/pyfaidx/__init__.py", line 118, in __getitem__
    raise ValueError("Coordinates start=%s and end=%s imply a diffent length than sequence (length %s)." % (self.start, self.end, len(self.seq)))
ValueError: Coordinates start=101 and end=100 imply a diffent length than sequence (length 0).

[mdshw5]

Thanks for pointing this out. I'll absolutely fix this since my goal for the project is to mimic Python sequence types as much as possible.

[mdshw5]

I sincerely forgot about this issue, and thanks to @prihoda for submitting a PR. Also thanks @dhauge for not only writing tests, but basing them on my existing test style. Thanks! Will close this issue as #155 provides a fix.