def index_repeatmasker_alignment_by_id(fh, out_fh, vebrose=False):
"""Build an index for a repeat-masker alignment file by repeat-masker ID."""
def extract_UID(rm_alignment):
return rm_alignment.meta[multipleAlignment.RM_ID_KEY]
index = IndexedFile(fh, repeat_masker_alignment_iterator, extract_UID)
index.write_index(out_fh)
def test_index_lookup(self, mock_open):
"""Test lookup of specific key using full UI."""
in_strm = StringIO.StringIO(self.ga_maf1)
idx_strm = StringIO.StringIO()
out_strm = StringIO.StringIO()
# replace open with mock
def open_side_effect(*args, **kwargs):
if not isinstance(args[0], basestring):
raise TypeError()
if args[0] == "one.maf":
return in_strm
elif args[0] == "one.idx":
return idx_strm
elif args[0] == "out.txt":
return out_strm
raise IOError("No such file")
mock_open.side_effect = open_side_effect
# build and index in idx_strm
bound_iter = functools.partial(genome_alignment_iterator,
reference_species="hg19")
hash_func = JustInTimeGenomeAlignmentBlock.build_hash
idx = IndexedFile(StringIO.StringIO(self.ga_maf1), bound_iter,
hash_func)
idx.write_index(idx_strm)
idx_strm.seek(0)
key = "chr22" + "\t" + "1772" + "\t" + "1825"
main(["lookup", "-o", "out.txt", "-k", key, "one.maf", "one.idx"])
self.assertEqual(
str(idx[key]).strip(),
str(out_strm.getvalue()).strip())
def index_genome_alignment_by_locus(fh, out_fh, verbose=False):
"""Build an index for a genome alig. using coords in ref genome as keys."""
bound_iter = functools.partial(genome_alignment_iterator,
reference_species="hg19", index_friendly=True)
hash_func = JustInTimeGenomeAlignmentBlock.build_hash
idx = IndexedFile(fh, bound_iter, hash_func)
idx.write_index(out_fh, verbose=verbose)
def index_repeatmasker_alignment_by_id(fh, out_fh, vebrose=False):
"""Build an index for a repeat-masker alignment file by repeat-masker ID."""
def extract_UID(rm_alignment):
return rm_alignment.meta[multipleAlignment.RM_ID_KEY]
index = IndexedFile(fh, repeat_masker_alignment_iterator, extract_UID)
index.write_index(out_fh)
def test_index_lookup(self, mock_open):
"""Test lookup of specific key using full UI."""
in_strm = StringIO.StringIO(self.ga_maf1)
idx_strm = StringIO.StringIO()
out_strm = StringIO.StringIO()
# replace open with mock
def open_side_effect(*args, **kwargs):
if not isinstance(args[0], basestring):
raise TypeError()
if args[0] == "one.maf":
return in_strm
elif args[0] == "one.idx":
return idx_strm
elif args[0] == "out.txt":
return out_strm
raise IOError("No such file")
mock_open.side_effect = open_side_effect
# build and index in idx_strm
bound_iter = functools.partial(genome_alignment_iterator,
reference_species="hg19")
hash_func = JustInTimeGenomeAlignmentBlock.build_hash
idx = IndexedFile(StringIO.StringIO(self.ga_maf1), bound_iter, hash_func)
idx.write_index(idx_strm)
idx_strm.seek(0)
key = "chr22" + "\t" + "1772" + "\t" + "1825"
main(["lookup", "-o", "out.txt", "-k", key, "one.maf", "one.idx"])
self.assertEqual(str(idx[key]).strip(), str(out_strm.getvalue()).strip())
def index_genome_alignment_by_locus(fh, out_fh, verbose=False):
"""Build an index for a genome alig. using coords in ref genome as keys."""
bound_iter = functools.partial(genome_alignment_iterator,
reference_species="hg19",
index_friendly=True)
hash_func = JustInTimeGenomeAlignmentBlock.build_hash
idx = IndexedFile(fh, bound_iter, hash_func)
idx.write_index(out_fh, verbose=verbose)
def _build_index(in_strng, ref_spec):
idx_strm = StringIO.StringIO()
bound_iter = functools.partial(genome_alignment_iterator,
reference_species=ref_spec)
hash_func = JustInTimeGenomeAlignmentBlock.build_hash
idx = IndexedFile(StringIO.StringIO(in_strng), bound_iter, hash_func)
idx.write_index(idx_strm)
idx_strm.seek(0) # seek to the start
return idx_strm
def _build_index(in_strng, ref_spec):
idx_strm = StringIO.StringIO()
bound_iter = functools.partial(genome_alignment_iterator,
reference_species=ref_spec)
hash_func = JustInTimeGenomeAlignmentBlock.build_hash
idx = IndexedFile(StringIO.StringIO(in_strng), bound_iter, hash_func)
idx.write_index(idx_strm)
idx_strm.seek(0) # seek to the start
return idx_strm
def _build_index(maf_strm, ref_spec):
"""Build an index for a MAF genome alig file and return StringIO of it."""
idx_strm = StringIO.StringIO()
bound_iter = functools.partial(genome_alignment_iterator,
reference_species=ref_spec)
hash_func = JustInTimeGenomeAlignmentBlock.build_hash
idx = IndexedFile(maf_strm, bound_iter, hash_func)
idx.write_index(idx_strm)
idx_strm.seek(0) # seek to the start
return idx_strm
def _build_index(maf_strm, ref_spec):
"""Build an index for a MAF genome alig file and return StringIO of it."""
idx_strm = StringIO.StringIO()
bound_iter = functools.partial(genome_alignment_iterator,
reference_species=ref_spec)
hash_func = JustInTimeGenomeAlignmentBlock.build_hash
idx = IndexedFile(maf_strm, bound_iter, hash_func)
idx.write_index(idx_strm)
idx_strm.seek(0) # seek to the start
return idx_strm
