def buildIndex(genome_fp, ref_genome_fp, genome_seq=None, ref_genome_seq=None,
fill_gaps=True, max_gap_width=300, smooth_edges=True,
smoothing_radius=20):
''' Builds and returns an index mapping from the genome in `genome_fp` to
the genome in `ref_genome_fp`. If `fillGaps` is True, gaps up to
`max_gap_width` will be filled if flanking indices can be found with
commensurate map spacing (see `fillGaps` docstring). If `smooth_edges` is
True, areas of high mismatch frequency with gap-penalty-related problems
will be smoothed.
'''
# Generate absolute filepaths
genome_fp = os.path.abspath(genome_fp)
ref_genome_fp = os.path.abspath(ref_genome_fp)
# Run mauve and parse output (all output files are cleaned up after run /
# parsing)
with TempDirs(1) as (temp_dir,):
output_fp = os.path.join(temp_dir, 'mauveout.xmfa')
runMauve([genome_fp, ref_genome_fp], flags={'--output': output_fp})
sub_alignment_groups = parseXMFA(output_fp)
genome_length = getGenomeLength(genome_fp)
# LUT to map indices from the engineered genome to the reference genome
idx_lut = np.empty(genome_length, dtype=IDX_ARRAY_DTYPE)
# Initialize all values to -1 (un-mapped indices will be -1)
idx_lut[:] = -1
# Parse sub-alignments into index mapping
for sub_alignment_group in sub_alignment_groups:
genome_sa = indexutils.lookupSubAlignment(1, sub_alignment_group)
ref_genome_sa = indexutils.lookupSubAlignment(2, sub_alignment_group)
if genome_sa is not None and ref_genome_sa is not None:
# Note that we have to convert to 0-based indexing
genome_idx = genome_sa.start_idx - 1
ref_genome_idx = ref_genome_sa.start_idx - 1
for idx, base in enumerate(genome_sa.seq):
ref_genome_base = ref_genome_sa.seq[idx]
if base != '-':
genome_idx += 1
if ref_genome_base != '-':
ref_genome_idx += 1
if base == ref_genome_base and genome_idx < genome_length:
idx_lut[genome_idx] = ref_genome_idx
if fill_gaps:
genome_seq = genome_seq or getSeqFromFile(genome_fp)
ref_genome_seq = ref_genome_seq or getSeqFromFile(ref_genome_fp)
indexutils.fixZeroIdx(idx_lut, genome_seq, ref_genome_seq)
indexutils.fillGaps(idx_lut, max_gap_width=max_gap_width)
if smooth_edges:
indexutils.smoothEdges(idx_lut, smoothing_radius=smoothing_radius)
return idx_lut
def getGenomeLength(genome_fp):
''' Return the genome length from a fasta file containing a single
header / sequence
'''
return len(getSeqFromFile(genome_fp))