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 get_exon_file_path (self):
'''
Retrieve the file with the ensembl exons in fasta format
'''
dc = DirectoryCrawler()
return "{0}/{1}.fa".format(dc.get_exon_ensembl_path(self.ref_protein_id), self.species)
