def test_top_contigs(self):
"""
Test top contigs from ref
"""
#ref_entry = ReferenceEntry.from_ref_dir(ref)
ref_entry = openReference(self.REFERENCE)
self.assertEqual(1, len(get_top_contigs_from_ref_entry(ref_entry, 2)))
def get_name_untruncator(repo_path, truncation_regex='\s'):
"""Return a dictionary that maps truncated reference names to full
reference names.
:param repo_path: Path to the reference repository that contains the
full reference names.
:param truncation_regex: Character at which reference names are truncated.
For SAM/BAM files, this is whitespace.
:returns: dict from truncated name to full name
:raises: ReferenceTruncationError if multiple full names truncate to the
same name.
"""
ref_entry = openReference(repo_path)
truncated_to_full = {}
for contig in ref_entry.contigs:
full_ref_name = contig.header
truncated_ref_name = re.split(truncation_regex, full_ref_name)[0]
if truncated_ref_name in truncated_to_full:
msg = ("The full reference '{r}' truncates to '{t}', "
"but another reference also truncates to '{t}'.".format(
r=full_ref_name, t=truncated_ref_name))
raise ReferenceTruncationError(msg)
truncated_to_full[truncated_ref_name] = full_ref_name
return truncated_to_full
def make_variants_report(aln_summ_gff, variants_gff, reference, max_contigs_to_plot, report, output_dir, dpi=72, dumpdata=True):
"""
Entry to report.
:param aln_summ_gff: (str) path to alignment_summary.gff
:param variants_gff: (str) path to variants_gff
:param reference: (str) path to reference_dir
:param max_contigs_to_plot: (int) max number of contigs to plot
"""
_validate_inputs([('aln_summ_gff', aln_summ_gff),
('variants_gff', variants_gff),
('reference', reference)])
# reference entry & top contings
ref = openReference(reference)
top_contigs = get_top_contigs_from_ref_entry(ref, max_contigs_to_plot)
# extract gff data from files
ref_data, contig_variants = _extract_alignment_summ_data(
aln_summ_gff, top_contigs)
_append_variants_gff_data(ref_data, variants_gff)
# make report objects
table, atts = _get_consensus_table_and_attributes(ref_data, ref)
plotgroup = _create_variants_plot_grp(
top_contigs, contig_variants, output_dir)
rpt = Report(Constants.R_ID,
plotgroups=[plotgroup],
attributes=atts,
tables=[table],
dataset_uuids=(ReferenceSet(reference).uuid,))
rpt = spec.apply_view(rpt)
rpt.write_json(os.path.join(output_dir, report))
return rpt
def get_name_untruncator(repo_path, truncation_regex='\s'):
"""Return a dictionary that maps truncated reference names to full
reference names.
:param repo_path: Path to the reference repository that contains the
full reference names.
:param truncation_regex: Character at which reference names are truncated.
For SAM/BAM files, this is whitespace.
:returns: dict from truncated name to full name
:raises: ReferenceTruncationError if multiple full names truncate to the
same name.
"""
ref_entry = openReference(repo_path)
truncated_to_full = {}
for contig in ref_entry.contigs:
full_ref_name = contig.header
truncated_ref_name = re.split(truncation_regex, full_ref_name)[0]
if truncated_ref_name in truncated_to_full:
msg = ("The full reference '{r}' truncates to '{t}', "
"but another reference also truncates to '{t}'."
.format(r=full_ref_name, t=truncated_ref_name))
raise ReferenceTruncationError(msg)
truncated_to_full[truncated_ref_name] = full_ref_name
return truncated_to_full
def test_top_contigs(self):
"""
Test top contigs from ref
"""
#ref_entry = ReferenceEntry.from_ref_dir(ref)
ref_entry = openReference(self.REFERENCE)
self.assertEqual(1, len(get_top_contigs_from_ref_entry(ref_entry, 2)))
def __init__(self, variantsGff, referenceDir, howMany=100, batchSortSize=10000):
"""varianstGff = source file, which can be a .gz; howMany = top N variants;
batchSortSize = the size of intermediate lists we sort.
referenceDir = referenceRepository dir, so we can fetch real contig names"""
self._howMany = howMany
self._batchSortSize = batchSortSize
self._variantsGff = variantsGff
self._rezip = False
self._reference = openReference(referenceDir)
def __init__(self,
variantsGff,
referenceDir,
howMany=100,
batchSortSize=10000):
"""varianstGff = source file, which can be a .gz; howMany = top N variants;
batchSortSize = the size of intermediate lists we sort.
referenceDir = referenceRepository dir, so we can fetch real contig names"""
self._howMany = howMany
self._batchSortSize = batchSortSize
self._variantsGff = variantsGff
self._rezip = False
self._reference = openReference(referenceDir)
def _get_reference_entry(self):
return openReference(self.REFERENCE)
def _get_reference_entry(self):
return openReference(self.REFERENCE)