#!/usr/bin/env python
'''Reads OTT files and produces a set of files with preorder
numbering that allow of minimal memory footprint in python scripts
Note: this script is a memory hog
'''
if __name__ == '__main__':
from peyotl.ott import OTT
ott = OTT()
ott.create_pickle_files()
def ott(self):
if self._ott is None:
self._ott = OTT(self.ott_dir)
return self._ott
def testTaxoRooting(self):
ott = OTT()
phylo = self.np.get_tree(tree_id='tree324')
evaluate_tree_rooting(self.nexson, ott, phylo)
help='use this flag to keep the OTT ids in addition to the names')
args = parser.parse_args()
print "converting {f}".format(f=args.newick_file)
print "using ott in {d}".format(d=args.ott_dir)
if (args.keep_ottids):
print "keeping OTT IDs in addition to names"
else:
print "replacing OTT IDs with names"
# read pruned labelled synthesis tree
ottpattern = re.compile(r"([(,)])(ott)(\d+)")
mrcapattern = re.compile(r"([(,)])mrcaott(\d+)ott(\d+)")
pos = 0
ott = OTT(ott_dir=args.ott_dir)
# load up the OTT dictionary...
d = ott.ott_id_to_names
outfile = codecs.open('ottnamelabelledtree.tre', 'w', encoding='utf-8')
with open(args.newick_file, 'r') as f:
newick = f.read()
for m in re.finditer(ottpattern, newick):
#print m.group(1),m.group(2),m.group(3)
ottid = int(m.group(3))
ottresults = d[ottid]
ottname = ottresults
if isinstance(ottresults, tuple):
ottname = ottresults[0]
print m.group(3), ottname
skippedchars = newick[pos:m.start()]
outfile.write(skippedchars)
def ott_shell_command(args):
ott = OTT()
_LOG.info('launching bash in your OTT dir...')
if subprocess.Popen('bash', cwd=ott.ott_dir).wait() != 0:
raise RuntimeError('bash in ott dir failed.')
def ott_clear_command(args):
ott = OTT()
ott.remove_caches()
