1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
|
from __future__ import absolute_import
# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE). http://etetoolkit.org
#
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ETE is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
# License for more details.
#
# You should have received a copy of the GNU General Public License
# along with ETE. If not, see <http://www.gnu.org/licenses/>.
#
#
# ABOUT THE ETE PACKAGE
# =====================
#
# ETE is distributed under the GPL copyleft license (2008-2015).
#
# If you make use of ETE in published work, please cite:
#
# Jaime Huerta-Cepas, Joaquin Dopazo and Toni Gabaldon.
# ETE: a python Environment for Tree Exploration. Jaime BMC
# Bioinformatics 2010,:24doi:10.1186/1471-2105-11-24
#
# Note that extra references to the specific methods implemented in
# the toolkit may be available in the documentation.
#
# More info at http://etetoolkit.org. Contact: huerta@embl.de
#
#
# #END_LICENSE#############################################################
import os
import logging
log = logging.getLogger("main")
from ..master_task import AlgTask
from ..master_job import Job
from ..utils import SeqGroup, OrderedDict, GLOBALS, pjoin
__all__ = ["Dialigntx"]
class Dialigntx(AlgTask):
def __init__(self, nodeid, multiseq_file, seqtype, conf, confname):
GLOBALS["citator"].add('dialigntx')
# fixed options for running this task
base_args = OrderedDict({
'': None,
})
# Initialize task
self.confname = confname
self.conf = conf
AlgTask.__init__(self, nodeid, "alg", "DialignTX",
base_args, self.conf[self.confname])
self.seqtype = seqtype
self.multiseq_file = multiseq_file
self.init()
def load_jobs(self):
# Only one Muscle job is necessary to run this task
appname = self.conf[self.confname]["_app"]
args = OrderedDict(self.args)
args[''] = "%s %s" %(pjoin(GLOBALS["input_dir"], self.multiseq_file),
"alg.fasta")
job = Job(self.conf["app"][appname], args, parent_ids=[self.nodeid])
job.add_input_file(self.multiseq_file)
self.jobs.append(job)
def finish(self):
# Once executed, alignment is converted into relaxed
# interleaved phylip format.
alg = SeqGroup(os.path.join(self.jobs[0].jobdir, "alg.fasta"))
fasta = alg.write(format="fasta")
phylip = alg.write(format="iphylip_relaxed")
AlgTask.store_data(self, fasta, phylip)
|
