def result(seq):
"""Returns True if seq adhers to the gap threshold and gap fraction."""
seq_gaps = array(seq.gapVector())
# check if gap amount bad
if sum(seq_gaps != template_gaps) / float(len(seq)) > gap_fraction:
return False
# check if gap runs bad
if "\x01" * gap_run in logical_and(seq_gaps, logical_not(template_gaps)).astype(UInt8).tostring():
return False
# check is insertion runs bad
elif "\x01" * gap_run in logical_and(template_gaps, logical_not(seq_gaps)).astype(UInt8).tostring():
return False
return True
def masked_to_unmasked(mask, remove_mask=False):
"""Returns array mapping indices in orig to indices in ungapped.
Specifically, for each position in orig, returns the index of the position
in the unmasked sequence of the last non-masked character at or before
that index (i.e. if the index corresponds to a masked position, will return
the index of the previous non-masked position since the masked positions
aren't in the unmasked sequence by definition).
If remove_mask is True (the default is False), sets the masked positions
to -1 for easy detection.
"""
result = cumsum(logical_not(mask)) -1
if remove_mask:
result = where(mask, -1, result)
return result
def unmasked_to_masked(mask):
"""Returns array mapping indices in ungapped to indices in original.
Any position where the mask is True will be omitted from the final result.
"""
return compress(logical_not(mask), arange(len(mask)))
