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 load_exons(self):
dc = DirectoryCrawler()
logger = Logger.Instance()
container_logger = logger.get_logger('containters')
exon_file_path = dc.get_exon_genewise_path(self.ref_protein_id)
exon_file_path += "/%s.fa" % self.species
if not os.path.isfile(exon_file_path):
container_logger.error ("{0},{1},genewise,no fasta file for genewise exons.".format(self.ref_protein_id, self.species))
return False
try:
exon_file = open(exon_file_path, 'r')
except IOError:
container_logger.error("%s,%s,%s" % (self.ref_protein_id, self.species, "No genewise exon file."))
return None
seq_records = SeqIO.parse(exon_file, "fasta", unambiguous_dna)
for seq_record in seq_records:
(num,ir1,ir2,data) = seq_record.description.split()
num = int(num)
(length, start, stop) = data.split('|')
exon = GenewiseExon((self.ref_protein_id, self.species), num, start, stop, seq_record.seq)
self.exons[num] = exon
return self.exons
def populate_sequence_exon_genewise(protein_id):
'''
Populates the "/PROTEIN_ID/sequence/exon/genewisel/<species>.fa"
folder with fasta files containing a list of all the exons for
a particular transcript. The data is acquired using the genewise
program.
This is used for the proteins found with an ab_initio method, that
dont have a list of exons on ensembl.
'''
logger = Logger.Instance()
alignment_logger = logger.get_logger('data_retrieval')
directory_crawler = DirectoryCrawler()
command_generator = CommandGenerator()
exon_genewise_path = directory_crawler.get_exon_genewise_path(protein_id)
try:
(proteins_known, proteins_abinitio) = DescriptionParser().parse_descr_file(protein_id)
except IOError, e:
alignment_logger.error("{0}, {1}, , {2}".format(protein_id, 'GENEWISE', e))
return
