def join(*args):
flags.assert_flag('sabmark-dir')
flags.assert_flag('sabmark-set')
if flags.config.sabmark_set == 'twilight':
return os.path.join(flags.config.sabmark_dir, __TWILIGHT, *args)
else:
return os.path.join(flags.config.sabmark_dir, __SUPERFAMILY, *args)
def search_bowdb_pdb(prot_files, bow_db=None, chain='',
limit=100, min=0.0, max=1.0):
flags.assert_flag('bow-db')
if bow_db is None:
bow_db = flags.config.bow_db
else:
bow_db = ejoin(bow_db)
if isinstance(prot_files, basestring):
prot_files = [prot_files]
file_hash = hashlib.md5(''.join(prot_files)).hexdigest()
outname = 'bowsearch_limit-%d_min-%f_max-%f_chain-%s_%s' \
% (limit, min, max, chain, file_hash)
outname = ejoin(outname)
def runsearch():
print >> open(outname, 'w+'), \
cmd('bowsearch', '-output', 'csv',
'-limit', '%d' % limit,
'-min', '%f' % min,
'-max', '%f' % max,
'--chain', chain,
bow_db, *prot_files)
cached([outname], runsearch)
print outname
rows = []
for row in csv.DictReader(open(outname), delimiter='\t'):
row['Cosine'] = float(row['Cosine'])
row['Euclid'] = float(row['Euclid'])
rows.append(row)
return rows
def join(*args):
flags.assert_flag('sabmark-dir')
flags.assert_flag('sabmark-set')
if flags.config.sabmark_set == 'twilight':
return os.path.join(flags.config.sabmark_dir, __TWILIGHT, *args)
else:
return os.path.join(flags.config.sabmark_dir, __SUPERFAMILY, *args)
def search_bowdb_pdb(prot_files,
bow_db=None,
chain='',
limit=100,
min=0.0,
max=1.0):
flags.assert_flag('bow-db')
if bow_db is None:
bow_db = flags.config.bow_db
else:
bow_db = ejoin(bow_db)
if isinstance(prot_files, basestring):
prot_files = [prot_files]
file_hash = hashlib.md5(''.join(prot_files)).hexdigest()
outname = 'bowsearch_limit-%d_min-%f_max-%f_chain-%s_%s' \
% (limit, min, max, chain, file_hash)
outname = ejoin(outname)
def runsearch():
print >> open(outname, 'w+'), \
cmd('bowsearch', '-output', 'csv',
'-limit', '%d' % limit,
'-min', '%f' % min,
'-max', '%f' % max,
'--chain', chain,
bow_db, *prot_files)
cached([outname], runsearch)
print outname
rows = []
for row in csv.DictReader(open(outname), delimiter='\t'):
row['Cosine'] = float(row['Cosine'])
row['Euclid'] = float(row['Euclid'])
rows.append(row)
return rows