def lookup_genome_alignment_index(index_fh, indexed_fh, out_fh=sys.stdout,
key=None, verbose=False):
"""Load a GA index and its indexed file and extract one or more blocks.
:param index_fh: the index file to load. Can be a filename or a
stream-like object.
:param indexed_fh: the file that the index was built for,
:param key: A single key, iterable of keys, or None. This key will be
used for lookup. If None, user is prompted to enter keys
interactively.
"""
# load the genome alignment as a JIT object
bound_iter = functools.partial(genome_alignment_iterator,
reference_species="hg19", index_friendly=True)
hash_func = JustInTimeGenomeAlignmentBlock.build_hash
idx = IndexedFile(record_iterator=bound_iter, record_hash_function=hash_func)
idx.read_index(index_fh, indexed_fh)
if key is None:
while key is None or key.strip() != "":
sys.stderr.write("[WAITING FOR KEY ENTRY ON STDIN; " +
"END WITH EMPTY LINE]\n")
key = raw_input()
# we know keys for genome alignments have tabs as delims, so..
key = '\t'.join(key.split()).strip()
if key != "":
out_fh.write(str(idx[key]) + "\n")
sys.stderr.write("\n")
else:
# we know keys for genome alignments have tabs as delims, so..
key = '\t'.join(key.split())
out_fh.write(str(idx[key]) + "\n")
def build_genome_alignment_from_file(ga_path, ref_spec, idx_path=None,
verbose=False):
"""
build a genome alignment by loading from a single MAF file.
:param ga_path: the path to the file to load.
:param ref_spec: which species in the MAF file is the reference?
:param idx_path: if provided, use this index to generate a just-in-time
genome alignment, instead of loading the file immediately.
"""
blocks = []
if (idx_path is not None):
bound_iter = functools.partial(genome_alignment_iterator,
reference_species=ref_spec)
hash_func = JustInTimeGenomeAlignmentBlock.build_hash
factory = IndexedFile(None, bound_iter, hash_func)
factory.read_index(idx_path, ga_path, verbose=verbose)
pind = None
for k in factory:
if verbose:
if pind is None:
total = len(factory)
pind = ProgressIndicator(totalToDo=total, messagePrefix="completed",
messageSuffix="building alignment blocks ")
pind.done += 1
pind.showProgress()
blocks.append(JustInTimeGenomeAlignmentBlock(factory, k))
else:
for b in genome_alignment_iterator(ga_path, ref_spec, verbose=verbose):
blocks.append(b)
return GenomeAlignment(blocks, verbose)
def lookup_genome_alignment_index(index_fh,
indexed_fh,
out_fh=sys.stdout,
key=None,
verbose=False):
"""Load a GA index and its indexed file and extract one or more blocks.
:param index_fh: the index file to load. Can be a filename or a
stream-like object.
:param indexed_fh: the file that the index was built for,
:param key: A single key, iterable of keys, or None. This key will be
used for lookup. If None, user is prompted to enter keys
interactively.
"""
# load the genome alignment as a JIT object
bound_iter = functools.partial(genome_alignment_iterator,
reference_species="hg19",
index_friendly=True)
hash_func = JustInTimeGenomeAlignmentBlock.build_hash
idx = IndexedFile(record_iterator=bound_iter,
record_hash_function=hash_func)
idx.read_index(index_fh, indexed_fh)
if key is None:
while key is None or key.strip() != "":
sys.stderr.write("[WAITING FOR KEY ENTRY ON STDIN; " +
"END WITH EMPTY LINE]\n")
key = raw_input()
# we know keys for genome alignments have tabs as delims, so..
key = '\t'.join(key.split()).strip()
if key != "":
out_fh.write(str(idx[key]) + "\n")
sys.stderr.write("\n")
else:
# we know keys for genome alignments have tabs as delims, so..
key = '\t'.join(key.split())
out_fh.write(str(idx[key]) + "\n")
def build_genome_alignment_from_file(ga_path,
ref_spec,
idx_path=None,
verbose=False):
"""
build a genome alignment by loading from a single MAF file.
:param ga_path: the path to the file to load.
:param ref_spec: which species in the MAF file is the reference?
:param idx_path: if provided, use this index to generate a just-in-time
genome alignment, instead of loading the file immediately.
"""
blocks = []
if (idx_path is not None):
bound_iter = functools.partial(genome_alignment_iterator,
reference_species=ref_spec)
hash_func = JustInTimeGenomeAlignmentBlock.build_hash
factory = IndexedFile(None, bound_iter, hash_func)
factory.read_index(idx_path, ga_path, verbose=verbose)
pind = None
for k in factory:
if verbose:
if pind is None:
total = len(factory)
pind = ProgressIndicator(
totalToDo=total,
messagePrefix="completed",
messageSuffix="building alignment blocks ")
pind.done += 1
pind.showProgress()
blocks.append(JustInTimeGenomeAlignmentBlock(factory, k))
else:
for b in genome_alignment_iterator(ga_path, ref_spec, verbose=verbose):
blocks.append(b)
return GenomeAlignment(blocks, verbose)
