def get_indexed_gene_types_matching_gtf_file_name(index_file_name, logger,
regex_str):
"""
Get gene structures contained in a GTF file whose file name matches regex_str
Because more than one species may match, returns a list of file names / gene_types
:param index_file_name: path to index file created by ``index_gtf_files(...)``
:type index_file_name: string
:param regex_str: regular expression used to match GTF file name by ``index_gtf_files(...)``
:type regex_str: string
:rtype list of tuples of (<matching identifier>, <original GTF path>, <dictionary of lists of genes>)
"""
index_data = _read_index_file(index_file_name)
regex = re.compile(regex_str)
results = []
#
# fields = <identifier><original_path><cache_path>
#
for id, original_gtf_path, gtf_cache_path in index_data:
m = regex.search(original_gtf_path)
if not m:
continue
gene_structures = gene.t_parse_gtf(id)
logger.info("Get indexed gene_types for %s from %s" %
(id, original_gtf_path))
results.append(
(id, original_gtf_path,
gene_structures.get_gene_types(original_gtf_path, gtf_cache_path,
logger)))
if not len(results):
logger.info(
"Regular expression %s did not match any entries in the index file %s"
% (regex_str, index_file_name))
return results
def get_indexed_gene_types_for_identifier(index_file_name, logger, identifier):
"""
Get gene structures contained in a GTF file whose file name matches identifier
:param index_file_name: path to index file created by ``index_gtf_files(...)``
:type index_file_name: string
:param identifier: identifier parsed from the GTF file name by ``index_gtf_files(...)``
:type identifier: string
:rtype tuple of (<matching identifier>, <original GTF path>, <dictionary of lists of genes>)
"""
index_data = sorted(_read_index_file(index_file_name), reverse=True)
all_ids = []
# go through in reverse order of id2 so that higher version numbers are retrieved first
for id, original_gtf_path, gtf_cache_path in index_data:
all_ids.append(id)
if id == identifier or id == identifier.replace(' ', '_'):
gene_structures = gene.t_parse_gtf(id)
logger.info("Get indexed genes for %s from %s" %
(id, original_gtf_path))
return (id, original_gtf_path,
gene_structures.get_gene_types(original_gtf_path,
gtf_cache_path, logger))
logger.info("Identifier %s was not found in the index file %s" %
(identifier, index_file_name))
return (None, all_ids, None)
def index_gtf_files(index_file_name, search_path_root, regex_input, cache_file_pattern,
identifier_pattern, ignore_cache = False, logger = None):
"""
Iterate through a directory, looking for all GTF files matching a regular expression.
Cache the GTF data to a file and write the location of the file to an index file
"""
if options.verbose > 1:
logger.debug("Using regular expression %s" % regex_input)
index_file = open(index_file_name, "w")
index_file_path = os.path.dirname(index_file_name)
regex = re.compile(regex_input)
for root, dirs, files in os.walk(search_path_root):
for file_name in files:
file_path = os.path.abspath(os.path.join(root, file_name))
m = regex.search(file_path)
if not m:
continue
if options.verbose > 1:
logger.debug("Indexing %s" % file_name)
cache_file_path = regex.sub(cache_file_pattern.format(INDEX_FILE_PATH = index_file_path),
file_path)
identifier = regex.sub(identifier_pattern , file_path)
index_file.write("%s\t%s\t%s\n" % (identifier, file_path, cache_file_path))
gene_structures = gene.t_parse_gtf(identifier)
if logger:
logger.debug("%s\t%s\t%s" % (identifier, file_path, cache_file_path))
gene_structures.index_genes (file_path, cache_file_path, logger, ignore_cache = ignore_cache)
def get_indexed_genes_matching_gtf_file_name(index_file_name, logger, regex_str):
"""
Get gene structures contained in a GTF file whose file name matches regex_str
Because more than one species may match, returns a list of file names / genes
:param index_file_name: path to index file created by ``index_gtf_files(...)``
:type index_file_name: string
:param regex_str: regular expression used to match GTF file name by ``index_gtf_files(...)``
:type regex_str: string
:rtype list of tuples of (<matching identifier>, <original GTF path>, <dictionary of lists of genes>)
"""
index_data = _read_index_file(index_file_name)
regex = re.compile(regex_str)
results = []
#
# fields = <identifier><original_path><cache_path>
#
for id, original_gtf_path, gtf_cache_path in index_data:
m = regex.search(original_gtf_path)
if not m:
continue
gene_structures = gene.t_parse_gtf(id)
logger.info("Get indexed genes for %s from %s" %
(id, original_gtf_path))
results.append((id, original_gtf_path,
gene_structures.get_genes(original_gtf_path, gtf_cache_path,
logger)))
if not len(results):
logger.info("Regular expression %s did not match any entries in the index file %s" %
(regex_str, index_file_name))
return results
def index_gtf_files(index_file_name,
search_path_root,
regex_input,
cache_file_pattern,
identifier_pattern,
ignore_cache=False,
logger=None):
"""
Iterate through a directory, looking for all GTF files matching a regular expression.
Cache the GTF data to a file and write the location of the file to an index file
"""
if options.verbose > 1:
logger.debug("Using regular expression %s" % regex_input)
index_file = open(index_file_name, "w")
index_file_path = os.path.dirname(index_file_name)
regex = re.compile(regex_input)
for root, dirs, files in os.walk(search_path_root):
for file_name in files:
file_path = os.path.abspath(os.path.join(root, file_name))
m = regex.search(file_path)
if not m:
continue
if options.verbose > 1:
logger.debug("Indexing %s" % file_name)
cache_file_path = regex.sub(
cache_file_pattern.format(INDEX_FILE_PATH=index_file_path),
file_path)
identifier = regex.sub(identifier_pattern, file_path)
index_file.write("%s\t%s\t%s\n" %
(identifier, file_path, cache_file_path))
gene_structures = gene.t_parse_gtf(identifier)
if logger:
logger.debug("%s\t%s\t%s" %
(identifier, file_path, cache_file_path))
gene_structures.index_genes(file_path,
cache_file_path,
logger,
ignore_cache=ignore_cache)
def get_indexed_genes_for_identifier(index_file_name, logger, identifier):
"""
Get gene structures contained in a GTF file whose file name matches identifier
:param index_file_name: path to index file created by ``index_gtf_files(...)``
:type index_file_name: string
:param identifier: identifier parsed from the GTF file name by ``index_gtf_files(...)``
:type identifier: string
:rtype tuple of (<matching identifier>, <original GTF path>, <dictionary of lists of genes>)
"""
index_data = sorted(_read_index_file(index_file_name), reverse = True)
all_ids = []
# go through in reverse order of id2 so that higher version numbers are retrieved first
for id, original_gtf_path, gtf_cache_path in index_data:
all_ids.append(id)
if id == identifier or id == identifier.replace(' ', '_'):
gene_structures = gene.t_parse_gtf(id)
logger.info("Get indexed genes for %s from %s" % (id, original_gtf_path))
return (id, original_gtf_path, gene_structures.get_genes(original_gtf_path, gtf_cache_path,
logger))
logger.info("Identifier %s was not found in the index file %s" %
(identifier, index_file_name))
return (None, all_ids, None)
