def test_assign_multiplty_spades_0(self, contig_collection_spades_0):
# Test how the function assigns multiplicity to contigs from
# file `test_contigs_spades_0.fasta
# "Rename" variable
contig_collection: cnt.ContigCollection
overlap_collection: ovl.OverlapCollection
contig_collection, overlap_collection = contig_collection_spades_0
# Assign
amu.assign_multiplty(contig_collection, overlap_collection)
expected_multplts: Sequence[float] = tuple([
1.0, # NODE_1
1.0, # NODE_2
1.8, # NODE_3
1.2 # NODE_4
])
obtained_multplts: Sequence[float] = tuple(
map(lambda x: x.multplty, contig_collection))
# Compare lengths
assert len(obtained_multplts) == len(expected_multplts)
# Compare multiplicities
for expected, obtained in zip(expected_multplts, obtained_multplts):
assert abs(obtained - expected) < 1e-1
def _do_combinator_work(infpath: str, mink: int,
maxk: int) -> MockContigsFixture:
# Read contigs
contig_collection: cnt.ContigCollection = cnt.get_contig_collection(
infpath, maxk)
# Detect adjacent contigs
overlap_collection: ovl.OverlapCollection = ovl.detect_adjacent_contigs(
contig_collection, mink, maxk)
# Assign multiplicity to contigs
amu.assign_multiplty(contig_collection, overlap_collection)
return contig_collection, overlap_collection
def main(version: str, last_update_date: str) -> None:
contigs_fpaths: Sequence[str] # paths to input files
params: Dict[str, Any] # parameters of the program
# Parse command line arguments
contigs_fpaths, params = parse_args(version, last_update_date)
# Report parameters of current run
_report_parameters(params, version, last_update_date)
# Iterate over input files and process them
fpath: str
for fpath in contigs_fpaths:
print('Processing file `{}`'.format(fpath))
# Create output dir
make_outdir(params['o'])
# Read contigs
contig_collection: cnt.ContigCollection = cnt.get_contig_collection(
fpath, params['a'])
# Detect adjacent contigs
overlap_collection: ovl.OverlapCollection = ovl.detect_adjacent_contigs(
contig_collection, params['i'], params['a'])
# Assign multiplicity to contigs
amu.assign_multiplty(contig_collection, overlap_collection)
# Make prefix for current input file
prefix: str = conf_prefix(fpath, params['o'])
# Write output files
# Write adjacency table
out.write_adjacency_table(contig_collection, overlap_collection,
params['o'], prefix)
# Write full log
out.write_full_log(contig_collection, overlap_collection, params['o'],
prefix)
# Write summary
out.write_summary(contig_collection, overlap_collection, fpath,
params['o'], prefix)
print('-' * 20)