def action(args):
if args.clobber and os.path.isdir(args.package_name):
try:
shutil.rmtree(args.package_name)
except:
print >> sys.stderr, "Failed: Could not delete %s" % args.package_name
return 1
elif args.clobber and os.path.exists(args.package_name):
try:
os.unlink(args.package_name)
except:
print >> sys.stderr, "Failed: Could not delete %s" % args.package_name
return 1
elif not args.clobber and os.path.exists(args.package_name):
print >> sys.stderr, 'Failed: {0} exists.'.format(args.package_name)
return 1
r = refpkg.Refpkg(args.package_name, create=True)
r.start_transaction()
r.update_metadata('locus', args.locus) # Locus is required
if args.description:
r.update_metadata('description', args.description)
if args.author:
r.update_metadata('author', args.author)
if args.package_version:
r.update_metadata('package_version', args.package_version)
if args.tree_stats:
r.update_phylo_model(args.stats_type,
args.tree_stats,
frequency_type=args.frequency_type)
for file_name in [
'aln_fasta', 'aln_sto', 'mask', 'profile', 'seq_info', 'taxonomy',
'tree', 'tree_stats', 'readme'
]:
path = getattr(args, file_name)
if path:
r.update_file(file_name, path)
r._log('Loaded initial files into empty refpkg')
r.commit_transaction()
r.strip()
reroot_prereqs = args.reroot and args.taxonomy and args.seq_info and args.tree
if utils.has_rppr(args.rppr) and reroot_prereqs:
r.start_transaction()
logging.info('%s found. Rerooting.', args.rppr)
r.reroot(rppr=args.rppr)
r._log('Rerooted')
r.commit_transaction()
elif reroot_prereqs:
log.warn('"%s" not found. Skipping rerooting', args.rppr)
return 0
def action(args):
if args.clobber and os.path.isdir(args.package_name):
try:
shutil.rmtree(args.package_name)
except:
print >>sys.stderr, "Failed: Could not delete %s" % args.package_name
return 1
elif args.clobber and os.path.exists(args.package_name):
try:
os.unlink(args.package_name)
except:
print >>sys.stderr, "Failed: Could not delete %s" % args.package_name
return 1
elif not args.clobber and os.path.exists(args.package_name):
print >> sys.stderr, 'Failed: {0} exists.'.format(args.package_name)
return 1
r = refpkg.Refpkg(args.package_name, create=True)
r.start_transaction()
r.update_metadata('locus', args.locus) # Locus is required
if args.description:
r.update_metadata('description', args.description)
if args.author:
r.update_metadata('author', args.author)
if args.package_version:
r.update_metadata('package_version', args.package_version)
if args.tree_stats:
r.update_phylo_model(args.stats_type, args.tree_stats,
frequency_type=args.frequency_type)
for file_name in ['aln_fasta', 'aln_sto', 'mask',
'profile', 'seq_info', 'taxonomy', 'tree', 'tree_stats',
'readme']:
path = getattr(args, file_name)
if path:
r.update_file(file_name, path)
r._log('Loaded initial files into empty refpkg')
r.commit_transaction()
r.strip()
reroot_prereqs = args.reroot and args.taxonomy and args.seq_info and args.tree
if utils.has_rppr(args.rppr) and reroot_prereqs:
r.start_transaction()
logging.info('%s found. Rerooting.', args.rppr)
r.reroot(rppr=args.rppr)
r._log('Rerooted')
r.commit_transaction()
elif reroot_prereqs:
log.warn('"%s" not found. Skipping rerooting', args.rppr)
return 0
import unittest
import tempfile
import shutil
import json
import copy
import os
import os.path
from taxtastic import refpkg, utils
from . import config
HAS_RPPR = utils.has_rppr()
class TestRefpkg(unittest.TestCase):
maxDiff = None
def test_fails_on_file_exists(self):
# Trying to attach to a normal file as a Refpkg should fail.
with tempfile.NamedTemporaryFile() as tf:
self.assertRaises(ValueError, refpkg.Refpkg, tf.name, create=False)
def test_fails_on_dir_without_manifest(self):
# Trying to attach to a non-Refpkg directory should fail.
with config.tempdir() as td:
self.assertRaises(ValueError, refpkg.Refpkg, td, create=False)
def test_create(self):
# Attaching to an empty directory should create a new, empty Refpkg.
scratch = tempfile.mkdtemp()
try:
import unittest
import tempfile
import shutil
import json
import copy
import os
import os.path
from taxtastic import refpkg, utils
from . import config
HAS_RPPR = utils.has_rppr()
class TestReadStockholm(unittest.TestCase):
def setUp(self):
self.fname = os.path.join(config.data_path('lactobacillus2-0.2.refpkg'),
'lactobacillus2.sto')
def test01(self):
with open(self.fname, 'r') as fobj:
names = utils.parse_stockholm(fobj)
self.assertEqual(len(names), 46)
self.assertEqual(names[0], '123f3-34')
self.assertEqual(names[-1], 'S000727873')
def test02(self):
with open(self.fname, 'r') as fobj:
lines = [line for line in fobj][:-1]
self.assertRaises(ValueError, utils.parse_stockholm, lines)