def get_itasser_models(self, homology_raw_dir, custom_itasser_name_mapping=None, outdir=None, force_rerun=False):
"""Copy generated I-TASSER models from a directory to the GEM-PRO directory.
Args:
homology_raw_dir (str): Root directory of I-TASSER folders.
custom_itasser_name_mapping (dict): Use this if your I-TASSER folder names differ from your model gene names.
Input a dict of {model_gene: ITASSER_folder}.
outdir (str): Path to output directory of downloaded files, must be set if GEM-PRO directories
were not created initially
force_rerun (bool): If homology files should be copied again even if they exist in the GEM-PRO directory
"""
counter = 0
for g in tqdm(self.genes):
if custom_itasser_name_mapping and g.id in custom_itasser_name_mapping:
hom_id = custom_itasser_name_mapping[g.id]
if not op.exists(op.join(homology_raw_dir, hom_id)):
hom_id = g.id
else:
hom_id = g.id
# The name of the actual pdb file will be $GENEID_model1.pdb
new_itasser_name = hom_id + '_model1'
orig_itasser_dir = op.join(homology_raw_dir, hom_id)
try:
itasser_prop = g.protein.load_itasser_folder(ident=hom_id, itasser_folder=orig_itasser_dir,
organize=True, outdir=outdir,
organize_name=new_itasser_name,
force_rerun=force_rerun)
except OSError:
log.debug('{}: homology model folder unavailable'.format(g.id))
continue
except IOError:
log.debug('{}: homology model unavailable'.format(g.id))
continue
if itasser_prop.structure_file:
counter += 1
else:
log.debug('{}: homology model file unavailable, perhaps modelling did not finish'.format(g.id))
log.info('Completed copying of {} I-TASSER models to GEM-PRO directory. See the "df_homology_models" attribute for a summary dataframe.'.format(counter))
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