class AlignmentTargetGenerator(object):
'''
Class used to retrieve the list of all possible targets from certain alignment
'''
def __init__(self):
self.crawler = DirectoryCrawler()
self.description_parser = DescriptionParser()
def get_blastn_targets(self, protein_id):
'''
@param protein_id: retrieves the list of species (RBS) not aligned with blastn for that protein
'''
path = self.crawler.get_blastn_path(protein_id)
return get_species_list(protein_id, path)
def set_failed_blastn_targets(self, protein_id, failed_species_list):
path = self.crawler.get_blastn_path(protein_id)
write_failed_species_to_status(failed_species_list, path)
def get_tblastn_targets(self, protein_id):
'''
@param protein_id: retrieves the list of species not aligned with tblastn for that protein
'''
path = self.crawler.get_tblastn_path(protein_id)
return get_species_list(protein_id, path)
def set_failed_tblastn_targets(self, protein_id, failed_species_list):
path = self.crawler.get_tblastn_path(protein_id)
write_failed_species_to_status(failed_species_list, path)
def get_SW_gene_targets(self, protein_id):
'''
@param protein_id: retrieves the list of species not aligned with SW_gene for that protein
'''
path = self.crawler.get_SW_gene_path(protein_id)
return get_species_list(protein_id, path)
def set_failed_SW_gene_targets(self, protein_id, failed_species_list):
path = self.crawler.get_SW_gene_path(protein_id)
write_failed_species_to_status(failed_species_list, path)
def get_SW_exon_targets(self, protein_id):
'''
@param protein_id: retrieves the list of species not aligned with SW_exon for that protein
'''
path = self.crawler.get_SW_exon_path(protein_id)
return get_species_list(protein_id, path)
def set_failed_SW_exon_targets(self, protein_id, failed_species_list):
path = self.crawler.get_SW_exon_path(protein_id)
write_failed_species_to_status(failed_species_list, path)
def reset_action (protein_id, key):
update_entry_in_status_file(protein_id, key, 'FAILED')
crawler = DirectoryCrawler()
if key == 'GENE_RETRIEVAL':
clear_directory(crawler.get_gene_path(protein_id))
elif key == 'EXP_GENE_RETRIEVAL' :
clear_directory(crawler.get_expanded_gene_path(protein_id))
elif key == 'PROTEIN_RETRIEVAL' :
clear_directory(crawler.get_protein_path(protein_id))
elif key == 'ENSEMBL_EXON_RETRIEVAL' :
clear_directory(crawler.get_exon_ensembl_path(protein_id))
elif key == 'GENEWISE_EXON_RETRIEVAL' :
clear_directory(crawler.get_exon_genewise_path(protein_id))
clear_directory(crawler.get_genewise_path(protein_id))
elif key == 'REF_SP_DB_FORMATTING' :
clear_directory(crawler.get_database_path(protein_id))
elif key == 'BLASTN_ALIGNMENT' :
clear_directory(crawler.get_blastn_path(protein_id))
elif key == 'TBLASTN_ALIGNMENT' :
clear_directory(crawler.get_tblastn_path(protein_id))
elif key == 'SW_GENE_ALIGNMENT' :
clear_directory(crawler.get_SW_gene_path(protein_id))
elif key == 'SW_EXON_ALIGNMENT' :
clear_directory(crawler.get_SW_exon_path(protein_id))
def parse_SW_output (ref_protein_id, species, sw_type):
'''
Parses the output from the SW# command line application.
(suitable for version as it was distributed on May 1st, 2012)
@param sw_type: sw_exon/sw_gene
@return: dictionary of alignment exons. The keys are referent exon IDs, and
values are lists of all the alignment exons which correspond to the certain
reference exon
'''
logger = Logger.Instance()
containers_logger = logger.get_logger('containers')
dc = DirectoryCrawler()
# determine the swout file path
if sw_type.lower() == "sw_gene":
swout_file_path = dc.get_SW_gene_path(ref_protein_id)
elif sw_type.lower() == "sw_exon":
swout_file_path = dc.get_SW_exon_path(ref_protein_id)
else:
raise KeyError ("There is no known swout path for type %s" % sw_type)
swout_file_path += "/%s.swout" % species
if not os.path.isfile(swout_file_path):
containers_logger.error ("{0}, {1}, {2}, no swout file".format(ref_protein_id, species, sw_type))
return False
swout_file = open(swout_file_path, 'r')
# status boolean variables
parsing_query_seq = True
# patterns for matching
header_pattern = re.compile ("Name: >(\d+)\|(\d+)\|(ENS\w+)\|(ENS\w+)\|([-]*1)")
#Intervals: 1207047 1207087 30 69 (+) strand
intervals_pattern = re.compile ("Intervals:\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+\([+-]\)\s+strand")
#Identity: 31/41 (75.6%)
identity_pattern = re.compile ("Identity:\s+(\d+)/(\d+).*")
#Similarity: 40/41 (97.6%)
similarity_pattern = re.compile ("Similarity:\s+(\d+)/.*")
#Gaps: 1/41 (2.4%)
gaps_pattern = re.compile ("Gaps:\s+(\d+)/\d+.*")
#Score: 2828.000
score_pattern = re.compile ("Score:.*")
# sequence pattern
sequence_pattern = re.compile ("\s*(\d+)\s+([ATCGN-]+)\s+(\d+).*")
exon_dict = {}
ref_exon_id = ""
identities = 0
positives = 0
gaps = 0
score = 0.
sbjct_start = 0
sbjct_end = 0
query_start = 0
query_end = 0
length = 0
query_sequence = ""
sbjct_sequence = ""
exon = Exon(sw_type, "", ref_protein_id, species)
for line in swout_file.readlines():
line = line.strip()
header_match = re.match(header_pattern, line)
if header_match:
#add the current exon and start a new one
if ref_exon_id:
exon.set_alignment_info(int(identities),
int(positives),
int(gaps),
int(sbjct_start),
int(sbjct_end),
int(query_start),
int(query_end),
int(length),
sbjct_sequence,
query_sequence,
float(score))
if ref_exon_id in exon_dict:
exon_dict[ref_exon_id].append(exon)
else:
exon_dict[ref_exon_id] = [exon]
ref_exon_id = header_match.groups()[3]
exon = Exon(sw_type, ref_exon_id, ref_protein_id, species)
parsing_query_seq = True
query_sequence = ""
sbjct_sequence = ""
# intervals
intervals_match = re.match (intervals_pattern, line)
if intervals_match:
(query_start, query_end, sbjct_start, sbjct_end) = intervals_match.groups()
# identities
identity_match = re.match (identity_pattern, line)
if identity_match:
(identities, length) = identity_match.groups()
# similarities
similarity_match = re.match(similarity_pattern, line)
if similarity_match:
positives = similarity_match.groups()[0]
# gaps
gaps_match = re.match (gaps_pattern, line)
if gaps_match:
gaps = gaps_match.groups()[0]
score_match = re.match(score_pattern, line)
if score_match:
score = line.split()[-1]
# sequence
sequence_match = re.match (sequence_pattern, line)
if sequence_match:
sequence_to_append = sequence_match.groups()[1].strip()
if parsing_query_seq:
query_sequence += sequence_to_append
parsing_query_seq = False
else:
sbjct_sequence += sequence_to_append
parsing_query_seq = True
exon.set_alignment_info(int(identities),
int(positives),
int(gaps),
int(sbjct_start),
int(sbjct_end),
int(query_start),
int(query_end),
int(length),
sbjct_sequence,
query_sequence,
float(score))
if query_sequence:
if ref_exon_id in exon_dict:
exon_dict[ref_exon_id].append(exon)
else:
exon_dict[ref_exon_id] = [exon]
return exon_dict
