def populate_SW_gene_alignments(protein_list):
for protein_id in protein_list:
if FileUtilities.read_status_file(protein_id)['EXP_GENE_RETRIEVAL'] == 'FAILED' or FileUtilities.read_status_file(protein_id)['REF_SP_DB_FORMATTING'] == 'FAILED':
print "ABORTING {0} SW_GENE: some resources have FAILED stats!".format(protein_id)
FileUtilities.update_entry_in_status_file(protein_id, 'SW_GENE_ALIGNMENT', 'FAILED')
continue
try:
if FileUtilities.read_status_file(protein_id)['SW_GENE_ALIGNMENT'] == 'OK':
print "SKIPPING {0} SW_GENE: .status file -> OK!".format(protein_id)
continue
except KeyError:
pass
print "ALIGNING SW_GENE: {0}".format(protein_id)
if Alignments.generate_SW_gene_alignments(protein_id):
FileUtilities.update_entry_in_status_file(protein_id, 'SW_GENE_ALIGNMENT', 'OK')
else:
FileUtilities.update_entry_in_status_file(protein_id, 'SW_GENE_ALIGNMENT', 'PARTIAL')
