def create_statistics(protein_list):
dc = DirectoryCrawler()
for (protein_id, exon_num) in protein_list:
stat_file = "%s/stats.csv" % dc.get_root_path(protein_id)
if not check_status_file(protein_id):
continue
create_protein_statistics(protein_id, stat_file)
class DescriptionParser:
"""
Loads configuration files from the cfg directory
"""
def __init__(self):
self.crawler = DirectoryCrawler()
def get_gene_regions(self, protein_id):
"""
Parses the description file for the protein_id, and retrieves the information about protein locations for every species.
Locations are stored as tuples (location_type, assembly, location_id, seq_begin, seq_end, strand)
@param protein_id: protein_id for which protein ids of other species should be retrieved
@return: (prot_ids_known, prot_ids_abinitio) - two dictionaries (key is species name, value is gene location data as described)
"""
(proteins_known, proteins_abinitio) = self.parse_descr_file(protein_id)
genes_known = {}
genes_abinitio = {}
for key, value in proteins_known.items():
genes_known[key] = list(value)[3:]
for key, value in proteins_abinitio.items():
genes_abinitio[key] = list(value)[1:]
return genes_known, genes_abinitio
def get_protein_ids(self, protein_id):
"""
Parses the description file for the protein_id, and retrieves only the protein ids for every species
@param protein_id: protein_id for which protein ids of other species should be retrieved
@return: (prot_ids_known, prot_ids_abinitio) - two dictionaries (key is species name, value is orthologous protein id)
"""
(proteins_known, proteins_abinitio) = self.parse_descr_file(protein_id)
prot_ids_known = {}
prot_ids_abinitio = {}
for key, value in proteins_known.items():
prot_ids_known[key] = list(value)[0]
for key, value in proteins_abinitio.items():
prot_ids_abinitio[key] = list(value)[0]
return prot_ids_known, prot_ids_abinitio
def get_species(self, protein_id):
"""
Parses the description file for the protein_id, and retrieves the list of species for which has reciprocal best search
found a valid protein.
@param protein_id: protein_id for which protein ids of other species should be retrieved
@return: species_list - found by RBH
"""
(proteins_known, proteins_abinitio) = self.parse_descr_file(protein_id)
species_list = proteins_known.keys()
species_list.extend(proteins_abinitio.keys())
for species in species_list:
species = species.strip()
return sorted(species_list)
def get_separated_species(self, protein_id):
(proteins_known, proteins_abinitio) = self.parse_descr_file(protein_id)
species_known = proteins_known.keys()
species_abinitio = proteins_abinitio.keys()
return (species_known, species_abinitio)
def get_strand_information(self, protein_id):
"""
Parses the description file for the protein_id and retrieves list of appropriate strands on which the proteins found by
RBH are found.
@param protein_id: protein_id for which protein ids of other species should be retrieved
@return: strands: dictionary (species:strand) - found by RBH
"""
strands = {}
(proteins_known, proteins_abinitio) = self.parse_descr_file(protein_id)
for (
species,
(spec_protein_id, gene_id, transcript_id, location_type, assembly, location_id, seq_begin, seq_end, strand),
) in proteins_known.items():
strands[species] = int(strand)
for (
species,
(spec_protein_id, location_type, assembly, location_id, seq_begin, seq_end, strand),
) in proteins_abinitio.items():
strands[species] = int(strand)
return strands
def parse_descr_file(self, protein_id):
"""
Function for parsing the description file associated with the protein_id.
Description file contains two different types of entries: for known protein and for abinitio.
Consequently, there are two formats that can be expected. They are both tab delimited.
known_format: species protein_id gene_id transcript_id location_type:assembly:location_id:seq_begin:seq_end:strand
abinitio_format: species protein_id location_type:assembly:location_id:seq_begin:seq_end:strand
@param protein_id: protein for which the description file will be parsed.
@return: proteins_known_data - dictionary (key is species, value is a tuple of all the available data for that species protein)
abinitio_known_data (the same), two dictionaries are returned as a tuple
(spec_protein_id, location_type, assembly, location_id, seq_begin, seq_end, strand)
@raise IOError: in case there is no description file present for the protein_id
"""
proteins_known_data = {}
proteins_abinitio_data = {}
descr_file_path = "{0}/{1}.descr".format(self.crawler.get_root_path(protein_id), protein_id)
pattern_known = re.compile("(.*)\t(ENS.*)\t(.*)\t(.*)\t(.*):(.*):(.*):(.*):(.*):(.*)")
pattern_abinitio = re.compile("(.*)\t(GEN.*)\t(.*):(.*):(.*):(.*):(.*):(.*)")
try:
descr_file = open(descr_file_path, "r")
except IOError:
raise IOError("There is no description file present for protein: %s" % protein_id)
for line in descr_file.readlines():
line = line.strip()
species_data = line.split()
if len(species_data) == 5:
species_name = species_data[0]
spec_protein_id, gene_id, transcript_id = species_data[1:4]
(location_type, assembly, location_id, seq_begin, seq_end, strand) = species_data[-1].split(":")
proteins_known_data[species_name] = (
spec_protein_id,
gene_id,
transcript_id,
location_type,
assembly,
location_id,
seq_begin,
seq_end,
strand,
)
elif len(species_data) == 3:
species_name = species_data[0]
(location_type, assembly, location_id, seq_begin, seq_end, strand) = species_data[-1].split(":")
spec_protein_id = species_data[1]
proteins_abinitio_data[species_name] = (
spec_protein_id,
location_type,
assembly,
location_id,
seq_begin,
seq_end,
strand,
)
descr_file.close()
return proteins_known_data, proteins_abinitio_data
def parse_description_file_general_info(self, protein_id):
"""
Similar as parse_description_file, but returns all the information. Required for generating a model structure.
known: (species_name, spec_protein_id, gene_id, transcript_id, location_type, assembly, location_id, seq_begin, seq_end, strand)
abinitio: (species_name, spec_protein_id, location_type, assembly, location_id, seq_begin, seq_end, strand)
"""
proteins_known_data = []
proteins_abinitio_data = []
descr_file_path = "{0}/{1}.descr".format(self.crawler.get_root_path(protein_id), protein_id)
pattern_known = re.compile("(.*)\t(ENS.*)\t(.*)\t(.*)\t(.*):(.*):(.*):(.*):(.*):(.*)")
pattern_abinitio = re.compile("(.*)\t(GEN.*)\t(.*):(.*):(.*):(.*):(.*):(.*)")
try:
descr_file = open(descr_file_path, "r")
except IOError:
raise IOError("There is no description file present for protein: %s" % protein_id)
for line in descr_file.readlines():
line = line.strip()
match = re.match(pattern_known, line)
if match:
(
species_name,
spec_protein_id,
gene_id,
transcript_id,
location_type,
assembly,
location_id,
seq_begin,
seq_end,
strand,
) = match.groups()
proteins_known_data.append(
(
species_name,
spec_protein_id,
gene_id,
transcript_id,
location_type,
assembly,
location_id,
seq_begin,
seq_end,
strand,
)
)
match = re.match(pattern_abinitio, line)
if match:
(
species_name,
spec_protein_id,
location_type,
assembly,
location_id,
seq_begin,
seq_end,
strand,
) = match.groups()
proteins_abinitio_data.append(
(species_name, spec_protein_id, location_type, assembly, location_id, seq_begin, seq_end, strand)
)
descr_file.close()
return proteins_known_data, proteins_abinitio_data
