def validate_reference_contig_coverage(ref_contigs, shared_contigs,
min_coverage_fraction):
"""Validates that shared_contigs spans a sufficient amount of ref_contigs.
Args:
ref_contigs: List of ContigInfo protos. All of the contigs from our
reference genome.
shared_contigs: The subset of ref_contigs that we found in common with
ref_contigs and all other genomics data sources.
min_coverage_fraction: The minimum fraction of basepairs of ref_contigs that
should be found among the shared_contigs.
Raises:
ValueError: If the fraction of covered bases is less than
min_coverage_fraction.
"""
def format_contig_matches():
pieces = []
common_map = ranges.contigs_dict(shared_contigs)
for ref_contig in ref_contigs:
status = 'matched' if ref_contig.name in common_map else 'IS MISSING'
pieces.append('"{}" is {} bp and {}'.format(ref_contig.name,
ref_contig.n_bases, status))
return ', '.join(pieces)
ref_bp = ranges.contigs_n_bases(ref_contigs)
common_bp = ranges.contigs_n_bases(shared_contigs)
coverage = common_bp / (1. * ref_bp)
if not shared_contigs or coverage < min_coverage_fraction:
raise ValueError('Reference contigs span {} bases but only {} bases '
'({:.2%}) were found in common among our input files. '
'Check that the sources were created on a common genome '
'reference build. Contig matches were: {}'.format(
ref_bp, common_bp, coverage, format_contig_matches()))
def test_contigs_n_bases(self): c1 = reference_pb2.ContigInfo(name='c', n_bases=100, pos_in_fasta=0) c2 = reference_pb2.ContigInfo(name='a', n_bases=50, pos_in_fasta=1) c3 = reference_pb2.ContigInfo(name='b', n_bases=25, pos_in_fasta=2) self.assertEqual(100, ranges.contigs_n_bases([c1])) self.assertEqual(50, ranges.contigs_n_bases([c2])) self.assertEqual(25, ranges.contigs_n_bases([c3])) self.assertEqual(150, ranges.contigs_n_bases([c1, c2])) self.assertEqual(125, ranges.contigs_n_bases([c1, c3])) self.assertEqual(175, ranges.contigs_n_bases([c1, c2, c3]))