def test_bedrecord__setters__3_fields():
record = BEDRecord("my_contig\t12\t345")
record.contig = "chrZ"
assert_equal(record.contig, "chrZ")
record.end += 20
assert_equal(record.end, 365)
assert_equal(str(record), "chrZ\t12\t365")
assert_equal(repr(record),
"BEDRecord(contig='chrZ', start=12, end=365)")
def test_bedrecord__setters__unset_fields__at_end():
record = BEDRecord("my_contig\t12\t345")
record.name = "my_region"
assert_equal(record.name, "my_region")
record.score = -13
assert_equal(record.score, -13)
record.strand = '-'
assert_equal(record.strand, '-')
assert_equal(str(record), "my_contig\t12\t345\tmy_region\t-13\t-")
assert_equal(repr(record),
"BEDRecord(contig='my_contig', start=12, end=345, "
"name='my_region', score=-13, strand='-')")
def _collect_and_validate_regions(regions):
contigs = _collect_fasta_contigs(regions)
sequences = set()
with open(regions["BED"]) as bedhandle:
for (line_num, line) in enumerate(bedhandle):
line = line.strip()
if not line or line.startswith("#"):
continue
try:
bed = BEDRecord(line)
except ValueError, error:
raise MakefileError(
("Error parsing line %i in regions file:\n"
" Path = %r\n Line = %r\n\n%s") %
(line_num + 1, regions["BED"], line, error))
if len(bed) < 6:
url = "http://genome.ucsc.edu/FAQ/FAQformat.html#format1"
name = repr(bed.name) if len(bed) > 3 else "unnamed record"
raise MakefileError(("Region at line #%i (%s) does not "
"contain the expected number of fields; "
"the first 6 fields are required. C.f. "
"defination at\n %s\n\nPath = %r") %
(line_num, name, url, regions["BED"]))
contig_len = contigs.get(bed.contig)
if contig_len is None:
raise MakefileError(("Regions file contains contig not found "
"in reference:\n Path = %r\n Contig = "
"%r\n\nPlease ensure that all contig "
"names match the reference names!") %
(regions["BED"], bed.contig))
elif not (0 <= bed.start < bed.end <= contig_len):
raise MakefileError(("Regions file contains invalid region:\n"
" Path = %r\n Contig = %r\n"
" Start = %s\n End = %s\n\n"
"Expected 0 <= Start < End <= %i!") %
(regions["BED"], bed.contig, bed.start,
bed.end, contig_len))
sequences.add(bed.name)
def _stat_areas_of_interest(cls, prefixes):
"""Returns (size, number of named intervals, total number of intervals)
for a set of areas of interest."""
areas_of_interest = {}
for (prefix_name, prefix) in prefixes.iteritems():
prefix_label = prefix.get("Label", prefix_name)
for (roi_name, roi_filename) in prefix.get("RegionsOfInterest", {}).iteritems():
count, names, size = 0, set(), 0
with open(roi_filename) as handle:
for line in handle:
bed = BEDRecord(line)
names.add(bed.name if len(bed) >= 4 else (bed.contig + "*"))
size += (bed.end - bed.start)
count += 1
areas_of_interest[(prefix_name, roi_name)] = {"Size" : size,
"NFeatures" : len(names),
"NIntervals" : count,
"Genome" : prefix["Name"],
"Name" : roi_name,
"Label" : "%s:%s" % (prefix_label, roi_name),
"Path" : roi_filename}
return areas_of_interest
def test_bedrecord__setters__unset_fields__after_end():
record = BEDRecord("")
record.strand = "-"
assert_equal(str(record), "\t0\t0\t\t0\t-")
record = BEDRecord("my_name")
record.strand = "-"
assert_equal(str(record), "my_name\t0\t0\t\t0\t-")
record = BEDRecord("my_name\t17")
record.strand = "-"
assert_equal(str(record), "my_name\t17\t0\t\t0\t-")
record = BEDRecord("my_name\t17\t258")
record.strand = "-"
assert_equal(str(record), "my_name\t17\t258\t\t0\t-")
record = BEDRecord("my_name\t17\t258\tregion")
record.strand = "-"
assert_equal(str(record), "my_name\t17\t258\tregion\t0\t-")
record = BEDRecord("my_name\t17\t258\tregion\t33")
record.strand = "-"
assert_equal(str(record), "my_name\t17\t258\tregion\t33\t-")
record = BEDRecord("my_name\t17\t258\tregion\t33\t+")
record.strand = "-"
assert_equal(str(record), "my_name\t17\t258\tregion\t33\t-")
