def repeat_masker_iterator(fh, alignment_index=None,
header=True, verbose=False):
"""
Iterator for repeatmasker coordinate annotation files. These files describe
the location of repeat occurrences. There is (optionally) a two-line header
with the names of the fields (ignored by the iterator, if present). Each line
is a record of an occurrence. The description of fields for each line is
given in from_repeat_masker_string.
:param fh: stream-like object, or string filename, to load the
annotations from
:param alignment_index: an IndexedFile for full alignments; keys should be
repeat-masker IDs
:param header: if True, expect and discard the two-line header;
otherwise we will expect there is no header
:param verbose: if True, output additional status messages about
progress to stderr.
"""
strm = fh
if type(fh).__name__ == "str":
strm = open(fh)
# try to get an idea of how much data we have...
if verbose:
try:
total = os.path.getsize(strm.name)
pind = ProgressIndicator(totalToDo=total, messagePrefix="completed",
messageSuffix="of processing " + strm.name)
except AttributeError as e:
sys.stderr.write(str(e))
sys.stderr.write("completed [unknown] of processing index")
verbose = False
if header:
# chomp first 2 lines
next(strm)
next(strm)
for line in strm:
if verbose:
pind.done = strm.tell()
pind.showProgress()
line = line.strip()
if line == "":
continue
rto = retrotransposon.from_repeat_masker_string(line)
if alignment_index is not None:
rto.pairwise_alignment =\
JustInTimePairwiseAlignment(alignment_index, rto.uniq_id)
yield rto
def test_basic_iterator(self):
elems = [x for x in repeat_masker_iterator(StringIO.StringIO(self.ann))]
self.assertEqual(len(elems), 6)
for i in range(0, len(elems)):
an = retrotransposon.from_repeat_masker_string(self.indv_an[i])
self.assertEqual(elems[i], an)
# alignments are not avaialble, so liftover should work only on coords;
# just check one to make sure its working
# elem[0]: 15, 67 -> 85, 141 - (53 to 57; gap_length = 14)
self.assertEqual(elems[0].liftover(GenomicInterval("chr1", 10, 100)),
[GenomicInterval("A#B", 128, 142, strand='+'),
GenomicInterval("A#B", 113, 127, strand='+'),
GenomicInterval("A#B", 98, 112, strand='+'),
GenomicInterval("A#B", 86, 97, strand='+')])
def test_iterator_with_alignment_index(self):
def extract_UID(rm_alignment):
return rm_alignment.meta[repeatmaskerAlignments.RM_ID_KEY]
s_io = StringIO.StringIO(self.rm_rc_1_input)
index = IndexedFile(s_io, repeat_masker_alignment_iterator, extract_UID)
elems = [x for x in repeat_masker_iterator(StringIO.StringIO(self.ann),
alignment_index=index)]
self.assertEqual(len(elems), 6)
for i in range(0, len(elems)):
an = retrotransposon.from_repeat_masker_string(self.indv_an[i])
self.assertEqual(elems[i], an)
# alignments were provided, liftover should be using them; test one
# to make sure they were matched up properly
r = elems[0].liftover(GenomicInterval("chr1", 10, 100))
self.assertEqual(r, [(132, 142), (120, 131), (88, 118), (85, 87)])
# also test one of the ones that had no alignment; here we expect failure
self.assertRaises(IndexError, elems[4].liftover,
GenomicInterval("chr1", 15200, 15400))
