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#!/usr/bin/env python
from os import remove
from cogent.util.unit_test import TestCase, main
from cogent.core.info import Info
from cogent.app.cmfinder import CMfinder,CombMotif
__author__ = "Shandy Wikman"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__contributors__ = ["Shandy Wikman"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Shandy Wikman"
__email__ = "ens01svn@cs.umu.se"
__status__ = "Development"
class CmfinderTest(TestCase):
"""Tests for Cmfinder application controller"""
def setUp(self):
self.input = cmfinder_input
def test_input_as_lines(self):
"""Test Cmfinder stdout input as lines"""
c = CMfinder(InputHandler='_input_as_lines')
res = c(self.input,remove_tmp=False)
#Filename in stdout, can't compare stdout since impossible to
#predict filename
self.assertEqual(res['ExitStatus'],0)
assert res['StdOut'] is not None
res.cleanUp()
def test_stdout_input_as_string(self):
"""Test Cmfinder stdout input as string"""
c = CMfinder()
exp ='%s\n' % '\n'.join([str(i).strip('\n') for i in cmfinder_stdout])
f = open('input.fasta','w')
txt = '\n'.join([str(i).strip('\n') for i in self.input])
f.write(txt)
f.close()
res = c('input.fasta',remove_tmp=False)
obs = res['StdOut'].read()
self.assertEqual(obs,exp)
self.assertEqual(res['ExitStatus'],0)
res.cleanUp()
remove('input.fasta')
def test_get_result_path(self):
"""Tests cmfinder result path"""
c =CMfinder(InputHandler='_input_as_lines')
res = c(self.input,remove_tmp=False)
self.assertEqualItems(res.keys(),['StdOut','StdErr','ExitStatus',
'cm_1','cm_2','cm_3','motif_1','motif_2','motif_3','latest',
'_input_filename'])
self.assertEqual(res['ExitStatus'],0)
assert res['cm_1'] is not None
assert res['cm_2'] is not None
assert res['cm_3'] is not None
assert res['motif_1'] is not None
assert res['motif_2'] is not None
assert res['motif_3'] is not None
res.cleanUp()
class CombMotifTest(TestCase):
"""Tests for CombMotif application controller
_input_as_lines function not used!!"""
def setUp(self):
""" """
a = open('input.fasta.cm.h1.1','w')
txt = '\n'.join([str(i).strip('\n') for i in cm1])
a.write(txt)
a.close()
b = open('input.fasta.cm.h1.2','w')
txt = '\n'.join([str(i).strip('\n') for i in cm2])
b.write(txt)
b.close()
c = open('input.fasta.cm.h1.3','w')
txt = '\n'.join([str(i).strip('\n') for i in cm3])
c.write(txt)
c.close()
d = open('input.fasta.motif.h1.1','w')
txt = '\n'.join([str(i).strip('\n') for i in motif1])
d.write(txt)
d.close()
e = open('input.fasta.motif.h1.2','w')
txt = '\n'.join([str(i).strip('\n') for i in motif2])
e.write(txt)
e.close()
f = open('input.fasta.motif.h1.3','w')
txt = '\n'.join([str(i).strip('\n') for i in motif3])
f.write(txt)
f.close()
g = open('input.fasta','w')
txt = '\n'.join([str(i).strip('\n') for i in cmfinder_input])
g.write(txt)
g.close()
def test_combmotif(self):
"""Tests CombMotif result path & input as string"""
cbm =CombMotif()
res = cbm('input.fasta')
self.assertEqualItems(res.keys(),['StdOut','StdErr','ExitStatus',
'comb1','latest'])
self.assertEqual(res['ExitStatus'],0)
assert res['comb1'] is not None
res.cleanUp()
remove('input.fasta')
remove('input.fasta.cm.h1.1')
remove('input.fasta.cm.h1.2')
remove('input.fasta.cm.h1.3')
remove('input.fasta.motif.h1.1')
remove('input.fasta.motif.h1.2')
remove('input.fasta.motif.h1.3')
remove('input.fasta.cm.h1.2.3')
cmfinder_input = ['>seq1\n', 'GGCTAGATAGCTCAGATGGTAGAGCAGAGGATTGAAGATCCTTGTGTCGTCGGTTCGATCCCGGCTCTGGCC\n', '>seq2\n', 'GGCTAGATAGCTCAGATGGTAGAGCAGAGGATTGAAGATCCTTGTGTCGTCGGTTCGATCCCGGCTCTGGCC\n', '>seq3\n', 'GGCTAGATAGCTCAGATGGTAGAGCAGAGGATTGAAGATCCTTGTGTCGTCGGTTCGATCCCGGCTCTGGCC\n', '>seq4\n', 'GGCTAGATAGCTCAGATGGTAGAGCAGAGGATTGAAGATCCTTGTGTCGTCGGTTCGATCCCGGCTCTGGCC']
cmfinder_stdout = ['Seq_0_Cand0_20_69 -0.000000\n', 'UAGAGCAGAGGAUUGAAGAUCCUUGUGUCGUCGGUUCGAUCCCGGCUCUG\n', '((((((...((((((((...((..........))))))))))..))))))\n', 'Seq_0_Cand1_29_61 -0.000000\n', 'GGAUUGAAGAUCCUUGUGUCGUCGGUUCGAUCC\n', '((((((((...((..........))))))))))\n', 'Seq_0_Cand2_36_68 -0.000000\n', 'AGAUCCUUGUGUCGUCGGUUCGAUCCCGGCUCU\n', '(((.((....((((......))))...)).)))\n', 'Alignment saved in file input.fasta.align.h1.1\n', 'Alignment saved in file input.fasta.align.h1.2\n', 'Alignment saved in file input.fasta.align.h1.3\n']
cm1 = ['INFERNAL-1 [0.7]\n', 'NAME (null)\n', 'STATES 154\n', 'NODES 40\n', 'W 200\n', 'el_selfsc 0.000000\n', 'NULL -0.363 -0.170 0.415 0.000 \n', 'MODEL:\n', '\t\t\t\t[ ROOT 0 ]\n', ' S 0 -1 0 1 4 -7.615 -7.822 -0.033 -6.236 \n', ' IL 1 1 2 1 4 -1.686 -2.369 -1.117 -4.855 1.023 -0.442 -0.708 -0.076 \n', ' IR 2 2 3 2 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 1 ]\n', ' ML 3 2 3 5 3 -8.950 -0.012 -7.267 -1.824 -2.170 -3.369 1.788 \n', ' D 4 2 3 5 3 -5.620 -0.734 -1.403 \n', ' IL 5 5 3 5 3 -1.925 -0.554 -4.164 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATR 2 ]\n', ' MR 6 5 3 8 5 -7.656 -0.026 -7.471 -7.683 -8.575 -1.639 -3.134 1.386 -2.615 \n', ' D 7 5 3 8 5 -5.352 -0.707 -2.978 -4.409 -2.404 \n', ' IR 8 8 3 8 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 3 ]\n', ' MP 9 8 3 13 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -3.884 -3.075 -5.228 4.065 -4.750 -5.113 -1.228 -4.059 -4.861 -0.314 -6.063 -1.931 -0.504 -4.796 -2.719 -3.753 \n', ' ML 10 8 3 13 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 11 8 3 13 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 12 8 3 13 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 13 13 5 13 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 14 14 6 14 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 4 ]\n', ' MP 15 14 6 19 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -6.059 -3.399 -7.491 -0.050 -6.698 -4.090 -1.804 -6.314 -5.110 3.545 -5.426 -1.969 -1.163 -4.250 -3.694 -5.400 \n', ' ML 16 14 6 19 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 17 14 6 19 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 18 14 6 19 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 19 19 5 19 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 20 20 6 20 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 5 ]\n', ' MP 21 20 6 25 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -3.884 -3.075 -5.228 4.065 -4.750 -5.113 -1.228 -4.059 -4.861 -0.314 -6.063 -1.931 -0.504 -4.796 -2.719 -3.753 \n', ' ML 22 20 6 25 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 23 20 6 25 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 24 20 6 25 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 25 25 5 25 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 26 26 6 26 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 6 ]\n', ' MP 27 26 6 31 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -6.059 -3.399 -7.491 -0.050 -6.698 -4.090 -1.804 -6.314 -5.110 3.545 -5.426 -1.969 -1.163 -4.250 -3.694 -5.400 \n', ' ML 28 26 6 31 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 29 26 6 31 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 30 26 6 31 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 31 31 5 31 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 32 32 6 32 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 7 ]\n', ' MP 33 32 6 37 4 -7.615 -7.822 -0.033 -6.236 -5.208 -5.325 -4.370 -0.894 -3.401 -4.617 3.483 -4.720 -7.134 -1.459 -5.156 -3.274 0.375 -6.308 -1.634 -4.773 \n', ' ML 34 32 6 37 4 -3.758 -3.940 -0.507 -2.670 1.023 -0.442 -0.708 -0.076 \n', ' MR 35 32 6 37 4 -4.809 -3.838 -1.706 -0.766 1.023 -0.442 -0.708 -0.076 \n', ' D 36 32 6 37 4 -4.568 -4.250 -2.265 -0.520 \n', ' IL 37 37 5 37 4 -1.686 -2.369 -1.117 -4.855 1.023 -0.442 -0.708 -0.076 \n', ' IR 38 38 6 38 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 8 ]\n', ' ML 39 38 6 41 3 -8.593 -0.013 -7.247 2.232 -3.180 -3.632 -2.819 \n', ' D 40 38 6 41 3 -6.174 -1.687 -0.566 \n', ' IL 41 41 3 41 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 9 ]\n', ' ML 42 41 3 44 3 -8.593 -0.013 -7.247 -1.639 -3.134 1.386 -2.615 \n', ' D 43 41 3 44 3 -6.174 -1.687 -0.566 \n', ' IL 44 44 3 44 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 10 ]\n', ' ML 45 44 3 47 3 -8.950 -0.012 -7.267 2.232 -3.180 -3.632 -2.819 \n', ' D 46 44 3 47 3 -5.620 -0.734 -1.403 \n', ' IL 47 47 3 47 3 -1.925 -0.554 -4.164 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATR 11 ]\n', ' MR 48 47 3 50 3 -8.950 -0.012 -7.267 -1.639 -3.134 1.386 -2.615 \n', ' D 49 47 3 50 3 -6.390 -1.568 -0.620 \n', ' IR 50 50 3 50 3 -1.925 -0.554 -4.164 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATR 12 ]\n', ' MR 51 50 3 53 5 -7.656 -0.026 -7.471 -7.683 -8.575 -2.124 1.984 -3.766 -2.279 \n', ' D 52 50 3 53 5 -5.352 -0.707 -2.978 -4.409 -2.404 \n', ' IR 53 53 3 53 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 13 ]\n', ' MP 54 53 3 58 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -6.059 -3.399 -7.491 -0.050 -6.698 -4.090 -1.804 -6.314 -5.110 3.545 -5.426 -1.969 -1.163 -4.250 -3.694 -5.400 \n', ' ML 55 53 3 58 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 56 53 3 58 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 57 53 3 58 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 58 58 5 58 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 59 59 6 59 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 14 ]\n', ' MP 60 59 6 64 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -6.059 -3.399 -7.491 -0.050 -6.698 -4.090 -1.804 -6.314 -5.110 3.545 -5.426 -1.969 -1.163 -4.250 -3.694 -5.400 \n', ' ML 61 59 6 64 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 62 59 6 64 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 63 59 6 64 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 64 64 5 64 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 65 65 6 65 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 15 ]\n', ' MP 66 65 6 70 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -3.884 -3.075 -5.228 4.065 -4.750 -5.113 -1.228 -4.059 -4.861 -0.314 -6.063 -1.931 -0.504 -4.796 -2.719 -3.753 \n', ' ML 67 65 6 70 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 68 65 6 70 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 69 65 6 70 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 70 70 5 70 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 71 71 6 71 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 16 ]\n', ' MP 72 71 6 76 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -3.687 -4.001 -5.006 -0.279 -3.289 -5.690 -0.341 -4.598 -4.707 -1.022 -5.894 -2.187 4.037 -4.560 -1.931 -3.750 \n', ' ML 73 71 6 76 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 74 71 6 76 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 75 71 6 76 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 76 76 5 76 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 77 77 6 77 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 17 ]\n', ' MP 78 77 6 82 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -4.629 -4.281 -5.803 -0.660 -4.305 -6.778 -1.192 -5.008 -5.286 -1.451 -6.272 -2.306 -0.329 -5.298 3.329 -4.356 \n', ' ML 79 77 6 82 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 80 77 6 82 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 81 77 6 82 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 82 82 5 82 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 83 83 6 83 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 18 ]\n', ' MP 84 83 6 88 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -6.059 -3.399 -7.491 -0.050 -6.698 -4.090 -1.804 -6.314 -5.110 3.545 -5.426 -1.969 -1.163 -4.250 -3.694 -5.400 \n', ' ML 85 83 6 88 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 86 83 6 88 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 87 83 6 88 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 88 88 5 88 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 89 89 6 89 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 19 ]\n', ' MP 90 89 6 94 4 -7.615 -7.822 -0.033 -6.236 -3.884 -3.075 -5.228 4.065 -4.750 -5.113 -1.228 -4.059 -4.861 -0.314 -6.063 -1.931 -0.504 -4.796 -2.719 -3.753 \n', ' ML 91 89 6 94 4 -3.758 -3.940 -0.507 -2.670 1.023 -0.442 -0.708 -0.076 \n', ' MR 92 89 6 94 4 -4.809 -3.838 -1.706 -0.766 1.023 -0.442 -0.708 -0.076 \n', ' D 93 89 6 94 4 -4.568 -4.250 -2.265 -0.520 \n', ' IL 94 94 5 94 4 -1.686 -2.369 -1.117 -4.855 1.023 -0.442 -0.708 -0.076 \n', ' IR 95 95 6 95 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 20 ]\n', ' ML 96 95 6 98 3 -8.593 -0.013 -7.247 2.232 -3.180 -3.632 -2.819 \n', ' D 97 95 6 98 3 -6.174 -1.687 -0.566 \n', ' IL 98 98 3 98 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 21 ]\n', ' ML 99 98 3 101 3 -8.593 -0.013 -7.247 -1.639 -3.134 1.386 -2.615 \n', ' D 100 98 3 101 3 -6.174 -1.687 -0.566 \n', ' IL 101 101 3 101 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 22 ]\n', ' ML 102 101 3 104 3 -8.593 -0.013 -7.247 2.232 -3.180 -3.632 -2.819 \n', ' D 103 101 3 104 3 -6.174 -1.687 -0.566 \n', ' IL 104 104 3 104 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 23 ]\n', ' ML 105 104 3 107 3 -8.593 -0.013 -7.247 -1.824 -2.170 -3.369 1.788 \n', ' D 106 104 3 107 3 -6.174 -1.687 -0.566 \n', ' IL 107 107 3 107 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 24 ]\n', ' ML 108 107 3 110 3 -8.593 -0.013 -7.247 -2.124 1.984 -3.766 -2.279 \n', ' D 109 107 3 110 3 -6.174 -1.687 -0.566 \n', ' IL 110 110 3 110 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 25 ]\n', ' ML 111 110 3 113 3 -8.593 -0.013 -7.247 -2.124 1.984 -3.766 -2.279 \n', ' D 112 110 3 113 3 -6.174 -1.687 -0.566 \n', ' IL 113 113 3 113 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 26 ]\n', ' ML 114 113 3 116 3 -8.593 -0.013 -7.247 -1.824 -2.170 -3.369 1.788 \n', ' D 115 113 3 116 3 -6.174 -1.687 -0.566 \n', ' IL 116 116 3 116 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 27 ]\n', ' ML 117 116 3 119 3 -8.593 -0.013 -7.247 -1.824 -2.170 -3.369 1.788 \n', ' D 118 116 3 119 3 -6.174 -1.687 -0.566 \n', ' IL 119 119 3 119 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 28 ]\n', ' ML 120 119 3 122 3 -8.593 -0.013 -7.247 -1.639 -3.134 1.386 -2.615 \n', ' D 121 119 3 122 3 -6.174 -1.687 -0.566 \n', ' IL 122 122 3 122 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 29 ]\n', ' ML 123 122 3 125 3 -8.593 -0.013 -7.247 -1.824 -2.170 -3.369 1.788 \n', ' D 124 122 3 125 3 -6.174 -1.687 -0.566 \n', ' IL 125 125 3 125 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 30 ]\n', ' ML 126 125 3 128 3 -8.593 -0.013 -7.247 -1.639 -3.134 1.386 -2.615 \n', ' D 127 125 3 128 3 -6.174 -1.687 -0.566 \n', ' IL 128 128 3 128 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 31 ]\n', ' ML 129 128 3 131 3 -8.593 -0.013 -7.247 -1.824 -2.170 -3.369 1.788 \n', ' D 130 128 3 131 3 -6.174 -1.687 -0.566 \n', ' IL 131 131 3 131 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 32 ]\n', ' ML 132 131 3 134 3 -8.593 -0.013 -7.247 -2.124 1.984 -3.766 -2.279 \n', ' D 133 131 3 134 3 -6.174 -1.687 -0.566 \n', ' IL 134 134 3 134 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 33 ]\n', ' ML 135 134 3 137 3 -8.593 -0.013 -7.247 -1.639 -3.134 1.386 -2.615 \n', ' D 136 134 3 137 3 -6.174 -1.687 -0.566 \n', ' IL 137 137 3 137 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 34 ]\n', ' ML 138 137 3 140 3 -8.593 -0.013 -7.247 -1.824 -2.170 -3.369 1.788 \n', ' D 139 137 3 140 3 -6.174 -1.687 -0.566 \n', ' IL 140 140 3 140 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 35 ]\n', ' ML 141 140 3 143 3 -8.593 -0.013 -7.247 -2.124 1.984 -3.766 -2.279 \n', ' D 142 140 3 143 3 -6.174 -1.687 -0.566 \n', ' IL 143 143 3 143 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 36 ]\n', ' ML 144 143 3 146 3 -8.593 -0.013 -7.247 -1.639 -3.134 1.386 -2.615 \n', ' D 145 143 3 146 3 -6.174 -1.687 -0.566 \n', ' IL 146 146 3 146 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 37 ]\n', ' ML 147 146 3 149 3 -8.593 -0.013 -7.247 -1.639 -3.134 1.386 -2.615 \n', ' D 148 146 3 149 3 -6.174 -1.687 -0.566 \n', ' IL 149 149 3 149 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 38 ]\n', ' ML 150 149 3 152 2 -9.084 -0.003 -1.824 -2.170 -3.369 1.788 \n', ' D 151 149 3 152 2 -8.445 -0.004 \n', ' IL 152 152 3 152 2 -1.823 -0.479 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ END 39 ]\n', ' E 153 152 3 -1 0 \n', '//\n']
cm2 = ['INFERNAL-1 [0.7]\n', 'NAME (null)\n', 'STATES 103\n', 'NODES 24\n', 'W 200\n', 'el_selfsc 0.000000\n', 'NULL -0.363 -0.170 0.415 0.000 \n', 'MODEL:\n', '\t\t\t\t[ ROOT 0 ]\n', ' S 0 -1 0 1 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 \n', ' IL 1 1 2 1 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 2 2 3 2 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 1 ]\n', ' MP 3 2 3 7 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -6.059 -3.399 -7.491 -0.050 -6.698 -4.090 -1.804 -6.314 -5.110 3.545 -5.426 -1.969 -1.163 -4.250 -3.694 -5.400 \n', ' ML 4 2 3 7 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 5 2 3 7 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 6 2 3 7 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 7 7 5 7 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 8 8 6 8 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 2 ]\n', ' MP 9 8 6 13 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -6.059 -3.399 -7.491 -0.050 -6.698 -4.090 -1.804 -6.314 -5.110 3.545 -5.426 -1.969 -1.163 -4.250 -3.694 -5.400 \n', ' ML 10 8 6 13 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 11 8 6 13 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 12 8 6 13 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 13 13 5 13 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 14 14 6 14 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 3 ]\n', ' MP 15 14 6 19 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -3.884 -3.075 -5.228 4.065 -4.750 -5.113 -1.228 -4.059 -4.861 -0.314 -6.063 -1.931 -0.504 -4.796 -2.719 -3.753 \n', ' ML 16 14 6 19 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 17 14 6 19 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 18 14 6 19 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 19 19 5 19 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 20 20 6 20 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 4 ]\n', ' MP 21 20 6 25 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -3.687 -4.001 -5.006 -0.279 -3.289 -5.690 -0.341 -4.598 -4.707 -1.022 -5.894 -2.187 4.037 -4.560 -1.931 -3.750 \n', ' ML 22 20 6 25 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 23 20 6 25 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 24 20 6 25 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 25 25 5 25 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 26 26 6 26 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 5 ]\n', ' MP 27 26 6 31 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -4.629 -4.281 -5.803 -0.660 -4.305 -6.778 -1.192 -5.008 -5.286 -1.451 -6.272 -2.306 -0.329 -5.298 3.329 -4.356 \n', ' ML 28 26 6 31 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 29 26 6 31 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 30 26 6 31 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 31 31 5 31 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 32 32 6 32 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 6 ]\n', ' MP 33 32 6 37 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -6.059 -3.399 -7.491 -0.050 -6.698 -4.090 -1.804 -6.314 -5.110 3.545 -5.426 -1.969 -1.163 -4.250 -3.694 -5.400 \n', ' ML 34 32 6 37 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 35 32 6 37 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 36 32 6 37 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 37 37 5 37 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 38 38 6 38 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 7 ]\n', ' MP 39 38 6 43 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -3.884 -3.075 -5.228 4.065 -4.750 -5.113 -1.228 -4.059 -4.861 -0.314 -6.063 -1.931 -0.504 -4.796 -2.719 -3.753 \n', ' ML 40 38 6 43 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 41 38 6 43 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 42 38 6 43 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 43 43 5 43 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 44 44 6 44 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 8 ]\n', ' MP 45 44 6 49 4 -7.487 -8.733 -0.052 -5.186 -3.884 -3.075 -5.228 4.065 -4.750 -5.113 -1.228 -4.059 -4.861 -0.314 -6.063 -1.931 -0.504 -4.796 -2.719 -3.753 \n', ' ML 46 44 6 49 4 -2.408 -4.532 -1.293 -1.473 1.023 -0.442 -0.708 -0.076 \n', ' MR 47 44 6 49 4 -4.102 -12.528 -0.390 -2.485 1.023 -0.442 -0.708 -0.076 \n', ' D 48 44 6 49 4 -12.737 -14.007 -2.036 -0.404 \n', ' IL 49 49 5 49 4 -2.817 -4.319 -0.613 -2.698 1.023 -0.442 -0.708 -0.076 \n', ' IR 50 50 6 50 3 -1.925 -0.554 -4.164 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATR 9 ]\n', ' MR 51 50 6 53 3 -8.950 -0.012 -7.267 -1.639 -3.134 1.386 -2.615 \n', ' D 52 50 6 53 3 -6.390 -1.568 -0.620 \n', ' IR 53 53 3 53 3 -1.925 -0.554 -4.164 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATR 10 ]\n', ' MR 54 53 3 56 5 -7.656 -0.026 -7.471 -7.683 -8.575 -1.639 -3.134 1.386 -2.615 \n', ' D 55 53 3 56 5 -5.352 -0.707 -2.978 -4.409 -2.404 \n', ' IR 56 56 3 56 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 11 ]\n', ' MP 57 56 3 61 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -6.059 -3.399 -7.491 -0.050 -6.698 -4.090 -1.804 -6.314 -5.110 3.545 -5.426 -1.969 -1.163 -4.250 -3.694 -5.400 \n', ' ML 58 56 3 61 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 59 56 3 61 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 60 56 3 61 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 61 61 5 61 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 62 62 6 62 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 12 ]\n', ' MP 63 62 6 67 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -3.884 -3.075 -5.228 4.065 -4.750 -5.113 -1.228 -4.059 -4.861 -0.314 -6.063 -1.931 -0.504 -4.796 -2.719 -3.753 \n', ' ML 64 62 6 67 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 65 62 6 67 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 66 62 6 67 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 67 67 5 67 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 68 68 6 68 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 13 ]\n', ' MP 69 68 6 73 4 -7.615 -7.822 -0.033 -6.236 -4.629 -4.281 -5.803 -0.660 -4.305 -6.778 -1.192 -5.008 -5.286 -1.451 -6.272 -2.306 -0.329 -5.298 3.329 -4.356 \n', ' ML 70 68 6 73 4 -3.758 -3.940 -0.507 -2.670 1.023 -0.442 -0.708 -0.076 \n', ' MR 71 68 6 73 4 -4.809 -3.838 -1.706 -0.766 1.023 -0.442 -0.708 -0.076 \n', ' D 72 68 6 73 4 -4.568 -4.250 -2.265 -0.520 \n', ' IL 73 73 5 73 4 -1.686 -2.369 -1.117 -4.855 1.023 -0.442 -0.708 -0.076 \n', ' IR 74 74 6 74 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 14 ]\n', ' ML 75 74 6 77 3 -8.593 -0.013 -7.247 -2.124 1.984 -3.766 -2.279 \n', ' D 76 74 6 77 3 -6.174 -1.687 -0.566 \n', ' IL 77 77 3 77 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 15 ]\n', ' ML 78 77 3 80 3 -8.593 -0.013 -7.247 -2.124 1.984 -3.766 -2.279 \n', ' D 79 77 3 80 3 -6.174 -1.687 -0.566 \n', ' IL 80 80 3 80 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 16 ]\n', ' ML 81 80 3 83 3 -8.593 -0.013 -7.247 -1.824 -2.170 -3.369 1.788 \n', ' D 82 80 3 83 3 -6.174 -1.687 -0.566 \n', ' IL 83 83 3 83 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 17 ]\n', ' ML 84 83 3 86 3 -8.593 -0.013 -7.247 -1.824 -2.170 -3.369 1.788 \n', ' D 85 83 3 86 3 -6.174 -1.687 -0.566 \n', ' IL 86 86 3 86 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 18 ]\n', ' ML 87 86 3 89 3 -8.593 -0.013 -7.247 -1.639 -3.134 1.386 -2.615 \n', ' D 88 86 3 89 3 -6.174 -1.687 -0.566 \n', ' IL 89 89 3 89 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 19 ]\n', ' ML 90 89 3 92 3 -8.593 -0.013 -7.247 -1.824 -2.170 -3.369 1.788 \n', ' D 91 89 3 92 3 -6.174 -1.687 -0.566 \n', ' IL 92 92 3 92 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 20 ]\n', ' ML 93 92 3 95 3 -8.593 -0.013 -7.247 -1.639 -3.134 1.386 -2.615 \n', ' D 94 92 3 95 3 -6.174 -1.687 -0.566 \n', ' IL 95 95 3 95 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 21 ]\n', ' ML 96 95 3 98 3 -8.593 -0.013 -7.247 -1.824 -2.170 -3.369 1.788 \n', ' D 97 95 3 98 3 -6.174 -1.687 -0.566 \n', ' IL 98 98 3 98 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 22 ]\n', ' ML 99 98 3 101 2 -9.084 -0.003 -2.124 1.984 -3.766 -2.279 \n', ' D 100 98 3 101 2 -8.445 -0.004 \n', ' IL 101 101 3 101 2 -1.823 -0.479 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ END 23 ]\n', ' E 102 101 3 -1 0 \n', '//\n']
cm3 = ['INFERNAL-1 [0.7]\n', 'NAME (null)\n', 'STATES 103\n', 'NODES 24\n', 'W 200\n', 'el_selfsc 0.000000\n', 'NULL -0.363 -0.170 0.415 0.000 \n', 'MODEL:\n', '\t\t\t\t[ ROOT 0 ]\n', ' S 0 -1 0 1 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 \n', ' IL 1 1 2 1 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 2 2 3 2 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 1 ]\n', ' MP 3 2 3 7 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -6.059 -3.399 -7.491 -0.050 -6.698 -4.090 -1.804 -6.314 -5.110 3.545 -5.426 -1.969 -1.163 -4.250 -3.694 -5.400 \n', ' ML 4 2 3 7 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 5 2 3 7 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 6 2 3 7 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 7 7 5 7 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 8 8 6 8 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 2 ]\n', ' MP 9 8 6 13 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -6.059 -3.399 -7.491 -0.050 -6.698 -4.090 -1.804 -6.314 -5.110 3.545 -5.426 -1.969 -1.163 -4.250 -3.694 -5.400 \n', ' ML 10 8 6 13 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 11 8 6 13 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 12 8 6 13 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 13 13 5 13 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 14 14 6 14 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 3 ]\n', ' MP 15 14 6 19 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -3.884 -3.075 -5.228 4.065 -4.750 -5.113 -1.228 -4.059 -4.861 -0.314 -6.063 -1.931 -0.504 -4.796 -2.719 -3.753 \n', ' ML 16 14 6 19 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 17 14 6 19 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 18 14 6 19 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 19 19 5 19 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 20 20 6 20 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 4 ]\n', ' MP 21 20 6 25 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -3.687 -4.001 -5.006 -0.279 -3.289 -5.690 -0.341 -4.598 -4.707 -1.022 -5.894 -2.187 4.037 -4.560 -1.931 -3.750 \n', ' ML 22 20 6 25 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 23 20 6 25 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 24 20 6 25 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 25 25 5 25 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 26 26 6 26 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 5 ]\n', ' MP 27 26 6 31 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -4.629 -4.281 -5.803 -0.660 -4.305 -6.778 -1.192 -5.008 -5.286 -1.451 -6.272 -2.306 -0.329 -5.298 3.329 -4.356 \n', ' ML 28 26 6 31 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 29 26 6 31 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 30 26 6 31 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 31 31 5 31 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 32 32 6 32 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 6 ]\n', ' MP 33 32 6 37 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -6.059 -3.399 -7.491 -0.050 -6.698 -4.090 -1.804 -6.314 -5.110 3.545 -5.426 -1.969 -1.163 -4.250 -3.694 -5.400 \n', ' ML 34 32 6 37 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 35 32 6 37 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 36 32 6 37 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 37 37 5 37 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 38 38 6 38 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 7 ]\n', ' MP 39 38 6 43 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -3.884 -3.075 -5.228 4.065 -4.750 -5.113 -1.228 -4.059 -4.861 -0.314 -6.063 -1.931 -0.504 -4.796 -2.719 -3.753 \n', ' ML 40 38 6 43 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 41 38 6 43 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 42 38 6 43 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 43 43 5 43 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 44 44 6 44 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 8 ]\n', ' MP 45 44 6 49 4 -7.487 -8.733 -0.052 -5.186 -3.884 -3.075 -5.228 4.065 -4.750 -5.113 -1.228 -4.059 -4.861 -0.314 -6.063 -1.931 -0.504 -4.796 -2.719 -3.753 \n', ' ML 46 44 6 49 4 -2.408 -4.532 -1.293 -1.473 1.023 -0.442 -0.708 -0.076 \n', ' MR 47 44 6 49 4 -4.102 -12.528 -0.390 -2.485 1.023 -0.442 -0.708 -0.076 \n', ' D 48 44 6 49 4 -12.737 -14.007 -2.036 -0.404 \n', ' IL 49 49 5 49 4 -2.817 -4.319 -0.613 -2.698 1.023 -0.442 -0.708 -0.076 \n', ' IR 50 50 6 50 3 -1.925 -0.554 -4.164 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATR 9 ]\n', ' MR 51 50 6 53 3 -8.950 -0.012 -7.267 -1.639 -3.134 1.386 -2.615 \n', ' D 52 50 6 53 3 -6.390 -1.568 -0.620 \n', ' IR 53 53 3 53 3 -1.925 -0.554 -4.164 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATR 10 ]\n', ' MR 54 53 3 56 5 -7.656 -0.026 -7.471 -7.683 -8.575 -1.639 -3.134 1.386 -2.615 \n', ' D 55 53 3 56 5 -5.352 -0.707 -2.978 -4.409 -2.404 \n', ' IR 56 56 3 56 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 11 ]\n', ' MP 57 56 3 61 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -6.059 -3.399 -7.491 -0.050 -6.698 -4.090 -1.804 -6.314 -5.110 3.545 -5.426 -1.969 -1.163 -4.250 -3.694 -5.400 \n', ' ML 58 56 3 61 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 59 56 3 61 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 60 56 3 61 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 61 61 5 61 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 62 62 6 62 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 12 ]\n', ' MP 63 62 6 67 6 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -3.884 -3.075 -5.228 4.065 -4.750 -5.113 -1.228 -4.059 -4.861 -0.314 -6.063 -1.931 -0.504 -4.796 -2.719 -3.753 \n', ' ML 64 62 6 67 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 1.023 -0.442 -0.708 -0.076 \n', ' MR 65 62 6 67 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 1.023 -0.442 -0.708 -0.076 \n', ' D 66 62 6 67 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n', ' IL 67 67 5 67 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 1.023 -0.442 -0.708 -0.076 \n', ' IR 68 68 6 68 5 -2.408 -0.496 -5.920 -4.087 -5.193 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATP 13 ]\n', ' MP 69 68 6 73 4 -7.615 -7.822 -0.033 -6.236 -4.629 -4.281 -5.803 -0.660 -4.305 -6.778 -1.192 -5.008 -5.286 -1.451 -6.272 -2.306 -0.329 -5.298 3.329 -4.356 \n', ' ML 70 68 6 73 4 -3.758 -3.940 -0.507 -2.670 1.023 -0.442 -0.708 -0.076 \n', ' MR 71 68 6 73 4 -4.809 -3.838 -1.706 -0.766 1.023 -0.442 -0.708 -0.076 \n', ' D 72 68 6 73 4 -4.568 -4.250 -2.265 -0.520 \n', ' IL 73 73 5 73 4 -1.686 -2.369 -1.117 -4.855 1.023 -0.442 -0.708 -0.076 \n', ' IR 74 74 6 74 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 14 ]\n', ' ML 75 74 6 77 3 -8.593 -0.013 -7.247 -2.124 1.984 -3.766 -2.279 \n', ' D 76 74 6 77 3 -6.174 -1.687 -0.566 \n', ' IL 77 77 3 77 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 15 ]\n', ' ML 78 77 3 80 3 -8.593 -0.013 -7.247 -2.124 1.984 -3.766 -2.279 \n', ' D 79 77 3 80 3 -6.174 -1.687 -0.566 \n', ' IL 80 80 3 80 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 16 ]\n', ' ML 81 80 3 83 3 -8.593 -0.013 -7.247 -1.824 -2.170 -3.369 1.788 \n', ' D 82 80 3 83 3 -6.174 -1.687 -0.566 \n', ' IL 83 83 3 83 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 17 ]\n', ' ML 84 83 3 86 3 -8.593 -0.013 -7.247 -1.824 -2.170 -3.369 1.788 \n', ' D 85 83 3 86 3 -6.174 -1.687 -0.566 \n', ' IL 86 86 3 86 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 18 ]\n', ' ML 87 86 3 89 3 -8.593 -0.013 -7.247 -1.639 -3.134 1.386 -2.615 \n', ' D 88 86 3 89 3 -6.174 -1.687 -0.566 \n', ' IL 89 89 3 89 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 19 ]\n', ' ML 90 89 3 92 3 -8.593 -0.013 -7.247 -1.824 -2.170 -3.369 1.788 \n', ' D 91 89 3 92 3 -6.174 -1.687 -0.566 \n', ' IL 92 92 3 92 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 20 ]\n', ' ML 93 92 3 95 3 -8.593 -0.013 -7.247 -1.639 -3.134 1.386 -2.615 \n', ' D 94 92 3 95 3 -6.174 -1.687 -0.566 \n', ' IL 95 95 3 95 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 21 ]\n', ' ML 96 95 3 98 3 -8.593 -0.013 -7.247 -1.824 -2.170 -3.369 1.788 \n', ' D 97 95 3 98 3 -6.174 -1.687 -0.566 \n', ' IL 98 98 3 98 3 -1.442 -0.798 -4.142 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ MATL 22 ]\n', ' ML 99 98 3 101 2 -9.084 -0.003 -2.124 1.984 -3.766 -2.279 \n', ' D 100 98 3 101 2 -8.445 -0.004 \n', ' IL 101 101 3 101 2 -1.823 -0.479 1.023 -0.442 -0.708 -0.076 \n', '\t\t\t\t[ END 23 ]\n', ' E 102 101 3 -1 0 \n', '//\n']
motif1 = ['# STOCKHOLM 1.0\n', '#=GF AU CMfinder 0.2\n', '\n', '#=GS seq1 WT 1.00\n', '#=GS seq2 WT 1.00\n', '#=GS seq3 WT 1.00\n', '#=GS seq4 WT 1.00\n', '\n', '#=GS seq1 DE 20.. 69\t89.835533\n', '#=GS seq2 DE 20.. 69\t89.835533\n', '#=GS seq3 DE 20.. 69\t89.835533\n', '#=GS seq4 DE 20.. 69\t89.835533\n', '\n', 'seq1 UAGAGCAGAGGAUUGAAGAUCCUUGUGUCGUCGGUUCGAUCCCGGCUCUG\n', '#=GR seq1 SS .<<<<<...<<<<<<<...................>>>>>>>..>>>>>.\n', 'seq2 UAGAGCAGAGGAUUGAAGAUCCUUGUGUCGUCGGUUCGAUCCCGGCUCUG\n', '#=GR seq2 SS .<<<<<...<<<<<<<...................>>>>>>>..>>>>>.\n', 'seq3 UAGAGCAGAGGAUUGAAGAUCCUUGUGUCGUCGGUUCGAUCCCGGCUCUG\n', '#=GR seq3 SS .<<<<<...<<<<<<<...................>>>>>>>..>>>>>.\n', 'seq4 UAGAGCAGAGGAUUGAAGAUCCUUGUGUCGUCGGUUCGAUCCCGGCUCUG\n', '#=GR seq4 SS .<<<<<...<<<<<<<...................>>>>>>>..>>>>>.\n', '#=GC SS_cons :<<<<<---<<<<<<<___________________>>>>>>>-->>>>>:\n', '#=GC RF UAGAGCAGAGGAUUGAAGAUCCUUGUGUCGUCGGUUCGAUCCCGGCUCUG\n', '//\n']
motif2 = ['# STOCKHOLM 1.0\n', '#=GF AU CMfinder 0.2\n', '\n', '#=GS seq1 WT 1.00\n', '#=GS seq2 WT 1.00\n', '#=GS seq3 WT 1.00\n', '#=GS seq4 WT 1.00\n', '\n', '#=GS seq1 DE 29.. 61\t59.381535\n', '#=GS seq2 DE 29.. 61\t59.381535\n', '#=GS seq3 DE 29.. 61\t59.381535\n', '#=GS seq4 DE 29.. 61\t59.381535\n', '\n', 'seq1 GGAUUGAAGAUCCUUGUGUCGUCGGUUCGAUCC\n', '#=GR seq1 SS <<<<<<<<<<<.........>>>..>>>>>>>>\n', 'seq2 GGAUUGAAGAUCCUUGUGUCGUCGGUUCGAUCC\n', '#=GR seq2 SS <<<<<<<<<<<.........>>>..>>>>>>>>\n', 'seq3 GGAUUGAAGAUCCUUGUGUCGUCGGUUCGAUCC\n', '#=GR seq3 SS <<<<<<<<<<<.........>>>..>>>>>>>>\n', 'seq4 GGAUUGAAGAUCCUUGUGUCGUCGGUUCGAUCC\n', '#=GR seq4 SS <<<<<<<<<<<.........>>>..>>>>>>>>\n', '#=GC SS_cons <<<<<<<<<<<_________>>>-->>>>>>>>\n', '#=GC RF GGAUUGAAGAUCCUUGUGUCGUCGGUUCGAUCC\n', '//\n']
motif3 = ['# STOCKHOLM 1.0\n', '#=GF AU CMfinder 0.2\n', '\n', '#=GS seq1 WT 1.00\n', '#=GS seq2 WT 1.00\n', '#=GS seq3 WT 1.00\n', '#=GS seq4 WT 1.00\n', '\n', '#=GS seq1 DE 36.. 68\t59.230255\n', '#=GS seq2 DE 36.. 68\t59.230255\n', '#=GS seq3 DE 36.. 68\t59.230255\n', '#=GS seq4 DE 36.. 68\t59.230255\n', '\n', 'seq1 AGAUCCUUGUGUCGUCGGUUCGAUCCCGGCUCU\n', '#=GR seq1 SS .<<........>><<<<<.......>>>>>...\n', 'seq2 AGAUCCUUGUGUCGUCGGUUCGAUCCCGGCUCU\n', '#=GR seq2 SS .<<........>><<<<<.......>>>>>...\n', 'seq3 AGAUCCUUGUGUCGUCGGUUCGAUCCCGGCUCU\n', '#=GR seq3 SS .<<........>><<<<<.......>>>>>...\n', 'seq4 AGAUCCUUGUGUCGUCGGUUCGAUCCCGGCUCU\n', '#=GR seq4 SS .<<........>><<<<<.......>>>>>...\n', '#=GC SS_cons :<<________>><<<<<_______>>>>>:::\n', '#=GC RF AGAUCCUUGUGUCGUCGGUUCGAUCCCGGCUCU\n', '//\n']
if __name__ == '__main__':
main()
|
