#!/usr/bin/env python
# test_infernal.py
from os import getcwd, remove, rmdir, mkdir, path
import tempfile, shutil
from cogent.core.moltype import DNA, RNA, PROTEIN
from cogent.core.alignment import DataError
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.infernal import Cmalign, Cmbuild, Cmcalibrate, Cmemit, Cmscore,\
Cmsearch, Cmstat, cmbuild_from_alignment, cmbuild_from_file, \
cmalign_from_alignment, cmalign_from_file, cmsearch_from_alignment,\
cmsearch_from_file
from cogent.parse.rfam import MinimalRfamParser, ChangedRnaSequence, \
ChangedSequence
from cogent.format.stockholm import stockholm_from_alignment
from cogent.struct.rna2d import ViennaStructure, wuss_to_vienna
__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Jeremy Widmann"]
__license__ = "GPL"
__version__ = "1.5.3-dev"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
__status__ = "Development"
class GeneralSetUp(TestCase):
def setUp(self):
"""Infernal general setUp method for all tests"""
self.seqs1_unaligned = {'1':'ACUGCUAGCUAGUAGCGUACGUA',\
'2':'GCUACGUAGCUAC',\
'3':'GCGGCUAUUAGAUCGUA'}
self.struct1_unaligned_string = '....(((...)))....'
self.seqs1_unaligned_gaps = {'1':'ACUGCUAGCUAGU-AGCGUAC--GUA',\
'2':'--GCUACGUAGCUAC',\
'3':'GCGGCUAUUAGAUCGUA--'}
self.seqs2_aligned = {'a': 'UAGGCUCUGAUAUAAUAGCUCUC---------',\
'c': '------------UGACUACGCAU---------',\
'b': '----UAUCGCUUCGACGAUUCUCUGAUAGAGA'}
self.seqs2_unaligned = {'a': 'UAGGCUCUGAUAUAAUAGCUCUC',\
'c': 'UGACUACGCAU',\
'b': 'UAUCGCUUCGACGAUUCUCUGAUAGAGA'}
self.struct2_aligned_string = '............((.(...)))..........'
self.struct2_aligned_dict = {'SS_cons':self.struct2_aligned_string}
self.lines2 = stockholm_from_alignment(aln=self.seqs2_aligned,\
GC_annotation=self.struct2_aligned_dict)
#self.seqs1 aligned to self.seqs2 with self.seqs2 included.
self.seqs1_and_seqs2_aligned = \
{'a': 'UAGGCUCUGAUAUAAUAGC-UCUC---------',\
'b': '----UAUCGCUUCGACGAU-UCUCUGAUAGAGA',\
'c': '------------UGACUAC-GCAU---------',\
'1': '-ACUGCUAGCUAGUAGCGUACGUA---------',\
'2': '----------GCUACGUAG-CUAC---------',\
'3': '-----GCGGCUAUUAG-AU-CGUA---------',\
}
self.seqs1_and_seqs2_aligned_struct_string = \
'............((.(....)))..........'
#self.seqs1 aligned to self.seqs2 without self.seqs2 included.
self.seqs1_aligned = \
{'1': 'ACUGCUAGCUAGUAGCGUACGUA',\
'2': '---------GCUACGUAG-CUAC',\
'3': '----GCGGCUAUUAG-AU-CGUA',\
}
self.seqs1_aligned_struct_string = \
'...........((.(....))).'
self.temp_dir = tempfile.mkdtemp()
self.temp_dir_spaces = '/tmp/test for infernal/'
try:
mkdir(self.temp_dir_spaces)
except OSError:
pass
try:
#create sequence files
f = open(path.join(self.temp_dir, 'seqs1.sto'),'w')
f.write(self.lines2)
f.close()
#create cm file.
self.cmfile = path.join(self.temp_dir, 'aln2.cm')
cm = open(self.cmfile,'w')
cm.write(ALN1_CM)
cm.close()
#create alignment file used to create cm file.
self.aln2_file = path.join(self.temp_dir, 'aln2.sto')
af = open(self.aln2_file,'w')
af.write(self.lines2)
af.close()
except OSError:
pass
class CmalignTests(GeneralSetUp):
"""Tests for the Cmalign application controller"""
def test_base_command(self):
"""Infernal BaseCommand should return the correct BaseCommand"""
c = Cmalign()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cmalign']))
c.Parameters['-l'].on()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cmalign -l']))
def test_changing_working_dir(self):
"""Infernal BaseCommand should change according to WorkingDir"""
c = Cmalign(WorkingDir='/tmp/cmalign_test')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/cmalign_test','/"; ','cmalign']))
c = Cmalign()
c.WorkingDir = '/tmp/cmalign_test2'
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/cmalign_test2','/"; ','cmalign']))
#removing the dirs is proof that they were created at the same time
#if the dirs are not there, an OSError will be raised
rmdir('/tmp/cmalign_test')
rmdir('/tmp/cmalign_test2')
def test_general_cleanUp(self):
"""Last test executed: cleans up all files initially created"""
# remove the tempdir and contents
shutil.rmtree(self.temp_dir)
shutil.rmtree(self.temp_dir_spaces)
def test_cmalign_from_alignment(self):
"""cmalign_from_alignment should work as expected.
"""
#Align with cmalign_from_alignment without original alignment.
aln, struct = cmalign_from_alignment(aln=self.seqs2_aligned,\
structure_string=self.struct2_aligned_string,\
seqs=self.seqs1_unaligned_gaps,moltype=RNA,include_aln=False)
#Check correct alignment
self.assertEqual(aln.todict(),self.seqs1_aligned)
#Check correct struct
self.assertEqual(wuss_to_vienna(str(struct)),\
self.seqs1_aligned_struct_string)
#should work with gapped seqs. Need to test this is taken care of
# since cmalign segfaults when there are gaps in the seqs to be aligned.
aln, struct = cmalign_from_alignment(aln=self.seqs2_aligned,\
structure_string=self.struct2_aligned_string,\
seqs=self.seqs1_unaligned_gaps,moltype=RNA)
#alignment should be correct
self.assertEqual(aln.todict(),self.seqs1_and_seqs2_aligned)
#structure should be correct
self.assertEqual(wuss_to_vienna(str(struct)),\
self.seqs1_and_seqs2_aligned_struct_string)
#should work with ungapped seqs.
aln, struct = cmalign_from_alignment(aln=self.seqs2_aligned,\
structure_string=self.struct2_aligned_string,\
seqs=self.seqs1_unaligned_gaps,moltype=RNA)
#alignment should be correct
self.assertEqual(aln.todict(),self.seqs1_and_seqs2_aligned)
#structure should be correct
self.assertEqual(wuss_to_vienna(str(struct)),\
self.seqs1_and_seqs2_aligned_struct_string)
#should return standard out
aln, struct,stdout = cmalign_from_alignment(aln=self.seqs2_aligned,\
structure_string=self.struct2_aligned_string,\
seqs=self.seqs1_unaligned_gaps,moltype=RNA,\
return_stdout=True)
#Test that standard out is same length as expected
self.assertEqual(len(stdout.split('\n')),\
len(CMALIGN_STDOUT.split('\n')))
def test_cmalign_from_file(self):
"""cmalign_from_file should work as expected.
"""
#Align with cmalign_from_file without original alignment.
aln,struct = cmalign_from_file(cm_file_path=self.cmfile,\
seqs=self.seqs1_unaligned,\
moltype=RNA)
#Check correct alignment
self.assertEqual(aln.todict(),self.seqs1_aligned)
#Check correct struct
self.assertEqual(wuss_to_vienna(str(struct)),\
self.seqs1_aligned_struct_string)
#Align with cmalign_from_file using original alignment.
aln,struct = cmalign_from_file(cm_file_path=self.cmfile,\
seqs=self.seqs1_unaligned,\
moltype=RNA,\
alignment_file_path=self.aln2_file,\
include_aln=True)
#alignment should be correct
self.assertEqual(aln.todict(),self.seqs1_and_seqs2_aligned)
#structure should be correct
self.assertEqual(wuss_to_vienna(str(struct)),\
self.seqs1_and_seqs2_aligned_struct_string)
class CmbuildTests(GeneralSetUp):
"""Tests for the Cmbuild application controller"""
def test_base_command(self):
"""Infernal BaseCommand should return the correct BaseCommand"""
c = Cmbuild()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cmbuild']))
c.Parameters['-A'].on()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cmbuild -A']))
def test_changing_working_dir(self):
"""Infernal BaseCommand should change according to WorkingDir"""
c = Cmbuild(WorkingDir='/tmp/cmbuild_test')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/cmbuild_test','/"; ','cmbuild']))
c = Cmbuild()
c.WorkingDir = '/tmp/cmbuild_test2'
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/cmbuild_test2','/"; ','cmbuild']))
#removing the dirs is proof that they were created at the same time
#if the dirs are not there, an OSError will be raised
rmdir('/tmp/cmbuild_test')
rmdir('/tmp/cmbuild_test2')
def test_general_cleanUp(self):
"""Last test executed: cleans up all files initially created"""
# remove the tempdir and contents
shutil.rmtree(self.temp_dir)
shutil.rmtree(self.temp_dir_spaces)
def test_cmbuild_from_alignment(self):
"""cmbuild_from_alignment should work as expected.
"""
#Test unaligned seqs and unaligned struct fail.
#DataError should be raised with Alignment is constructed
self.assertRaises(DataError,cmbuild_from_alignment,\
self.seqs1_unaligned,self.struct1_unaligned_string)
#Test aligned seqs and unaligned struct fail.
self.assertRaises(ValueError,cmbuild_from_alignment,\
self.seqs2_aligned,self.struct1_unaligned_string)
#Test get cm back without alignment.
cm_res = cmbuild_from_alignment(self.seqs2_aligned,\
self.struct2_aligned_string)
cm_lines = cm_res.split('\n')
ALN1_CM_lines = ALN1_CM.split('\n')
#Check that the same number of lines are in both CMs
self.assertEqual(len(cm_lines),len(ALN1_CM_lines))
#The first 13 lines are unique to the specific run. The res of the
# CM should be the same, since built from the same data.
self.assertEqual(cm_lines[13:],ALN1_CM_lines[13:])
#Make sure same alignment is returned if return_alignment=True
cm_res, cm_aln = cmbuild_from_alignment(self.seqs2_aligned,\
self.struct2_aligned_string,return_alignment=True)
self.assertEqual(cm_aln,self.lines2)
def test_cmbuild_from_file(self):
"""cmbuild_from_file should work as expected.
"""
cm_res = cmbuild_from_file(self.temp_dir+'/seqs1.sto')
cm_lines = cm_res.split('\n')
ALN1_CM_lines = ALN1_CM.split('\n')
#Check that the same number of lines are in both CMs
self.assertEqual(len(cm_lines),len(ALN1_CM_lines))
#The first 13 lines are unique to the specific run. The res of the
# CM should be the same, since built from the same data.
self.assertEqual(cm_lines[13:],ALN1_CM_lines[13:])
#Make sure same alignment is returned if return_alignment=True
cm_res, cm_aln = cmbuild_from_alignment(self.seqs2_aligned,\
self.struct2_aligned_string,return_alignment=True)
self.assertEqual(cm_aln,self.lines2)
class CmcalibrateTests(GeneralSetUp):
"""Tests for the Cmcalibrate application controller"""
def test_base_command(self):
"""Infernal BaseCommand should return the correct BaseCommand"""
c = Cmcalibrate()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cmcalibrate']))
c.Parameters['--mpi'].on()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cmcalibrate --mpi']))
def test_changing_working_dir(self):
"""Infernal BaseCommand should change according to WorkingDir"""
c = Cmcalibrate(WorkingDir='/tmp/cmcalibrate_test')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/cmcalibrate_test','/"; ','cmcalibrate']))
c = Cmcalibrate()
c.WorkingDir = '/tmp/cmcalibrate_test2'
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/cmcalibrate_test2','/"; ','cmcalibrate']))
#removing the dirs is proof that they were created at the same time
#if the dirs are not there, an OSError will be raised
rmdir('/tmp/cmcalibrate_test')
rmdir('/tmp/cmcalibrate_test2')
def test_general_cleanUp(self):
"""Last test executed: cleans up all files initially created"""
# remove the tempdir and contents
shutil.rmtree(self.temp_dir)
shutil.rmtree(self.temp_dir_spaces)
class CmemitTests(GeneralSetUp):
"""Tests for the Cmemit application controller"""
def test_base_command(self):
"""Infernal BaseCommand should return the correct BaseCommand"""
c = Cmemit()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cmemit']))
c.Parameters['-u'].on()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cmemit -u']))
def test_changing_working_dir(self):
"""Infernal BaseCommand should change according to WorkingDir"""
c = Cmemit(WorkingDir='/tmp/cmemit_test')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/cmemit_test','/"; ','cmemit']))
c = Cmemit()
c.WorkingDir = '/tmp/cmemit_test2'
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/cmemit_test2','/"; ','cmemit']))
#removing the dirs is proof that they were created at the same time
#if the dirs are not there, an OSError will be raised
rmdir('/tmp/cmemit_test')
rmdir('/tmp/cmemit_test2')
def test_general_cleanUp(self):
"""Last test executed: cleans up all files initially created"""
# remove the tempdir and contents
shutil.rmtree(self.temp_dir)
shutil.rmtree(self.temp_dir_spaces)
class CmscoreTests(GeneralSetUp):
"""Tests for the Cmscore application controller"""
def test_base_command(self):
"""Infernal BaseCommand should return the correct BaseCommand"""
c = Cmscore()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cmscore']))
c.Parameters['-l'].on()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cmscore -l']))
def test_changing_working_dir(self):
"""Infernal BaseCommand should change according to WorkingDir"""
c = Cmscore(WorkingDir='/tmp/cmscore_test')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/cmscore_test','/"; ','cmscore']))
c = Cmscore()
c.WorkingDir = '/tmp/cmscore_test2'
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/cmscore_test2','/"; ','cmscore']))
#removing the dirs is proof that they were created at the same time
#if the dirs are not there, an OSError will be raised
rmdir('/tmp/cmscore_test')
rmdir('/tmp/cmscore_test2')
def test_general_cleanUp(self):
"""Last test executed: cleans up all files initially created"""
# remove the tempdir and contents
shutil.rmtree(self.temp_dir)
shutil.rmtree(self.temp_dir_spaces)
class CmsearchTests(GeneralSetUp):
"""Tests for the Cmsearch application controller"""
def test_base_command(self):
"""Infernal BaseCommand should return the correct BaseCommand"""
c = Cmsearch()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cmsearch']))
c.Parameters['-p'].on()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cmsearch -p']))
def test_changing_working_dir(self):
"""Infernal BaseCommand should change according to WorkingDir"""
c = Cmsearch(WorkingDir='/tmp/cmsearch_test')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/cmsearch_test','/"; ','cmsearch']))
c = Cmsearch()
c.WorkingDir = '/tmp/cmsearch_test2'
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/cmsearch_test2','/"; ','cmsearch']))
#removing the dirs is proof that they were created at the same time
#if the dirs are not there, an OSError will be raised
rmdir('/tmp/cmsearch_test')
rmdir('/tmp/cmsearch_test2')
def test_general_cleanUp(self):
"""Last test executed: cleans up all files initially created"""
# remove the tempdir and contents
shutil.rmtree(self.temp_dir)
shutil.rmtree(self.temp_dir_spaces)
def test_cmsearch_from_alignment_no_hits(self):
"""cmsearch_from_alignment should work as expected
"""
search_res = cmsearch_from_alignment(aln=self.seqs2_aligned,\
structure_string=self.struct2_aligned_string,\
seqs=self.seqs1_unaligned,moltype=RNA)
self.assertEqual(search_res,[])
def test_cmsearch_from_alignment(self):
"""cmsearch_from_alignment should work as expected
"""
exp_search_res = [['a', 5, 23, 1, 19, 12.85, '-', 37],\
['b', 1, 19, 1, 19, 14.359999999999999, '-', 47]]
search_res = cmsearch_from_alignment(aln=self.seqs2_aligned,\
structure_string=self.struct2_aligned_string,\
seqs=self.seqs2_unaligned,moltype=RNA)
for search, exp in zip(search_res, exp_search_res):
self.assertEqual(search[1:],exp)
def test_cmsearch_from_file_no_hits(self):
"""cmsearch_from_file should work as expected
"""
search_res = cmsearch_from_file(cm_file_path=self.cmfile,\
seqs=self.seqs1_unaligned,moltype=RNA)
self.assertEqual(search_res,[])
def test_cmsearch_from_file(self):
"""cmsearch_from_file should work as expected
"""
exp_search_res = [['a', 5, 23, 1, 19, 12.85, '-', 37],\
['b', 1, 19, 1, 19, 14.359999999999999, '-', 47]]
search_res = cmsearch_from_file(cm_file_path=self.cmfile,\
seqs=self.seqs2_unaligned,moltype=RNA)
for search, exp in zip(search_res, exp_search_res):
self.assertEqual(search[1:],exp)
class CmstatTests(GeneralSetUp):
"""Tests for the Cmstat application controller"""
def test_base_command(self):
"""Infernal BaseCommand should return the correct BaseCommand"""
c = Cmstat()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cmstat']))
c.Parameters['-g'].on()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','cmstat -g']))
def test_changing_working_dir(self):
"""Infernal BaseCommand should change according to WorkingDir"""
c = Cmstat(WorkingDir='/tmp/cmstat_test')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/cmstat_test','/"; ','cmstat']))
c = Cmstat()
c.WorkingDir = '/tmp/cmstat_test2'
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/cmstat_test2','/"; ','cmstat']))
#removing the dirs is proof that they were created at the same time
#if the dirs are not there, an OSError will be raised
rmdir('/tmp/cmstat_test')
rmdir('/tmp/cmstat_test2')
def test_general_cleanUp(self):
"""Last test executed: cleans up all files initially created"""
# remove the tempdir and contents
shutil.rmtree(self.temp_dir)
shutil.rmtree(self.temp_dir_spaces)
ALN1_CM = """INFERNAL-1 [1.0rc1]
NAME aln1-1
STATES 61
NODES 18
ALPHABET 1
ELSELF -0.08926734
WBETA 1e-07
NSEQ 3
EFFNSEQ 3.000
CLEN 19
BCOM cmbuild aln1.cm aln1.sto
BDATE Sun Oct 5 18:45:35 2008
NULL 0.000 0.000 0.000 0.000
MODEL:
[ ROOT 0 ]
S 0 -1 0 1 4 -2.071 -2.210 -1.649 -2.140
IL 1 1 2 1 4 -0.556 -5.022 -1.818 -7.508 0.000 0.000 0.000 0.000
IR 2 2 3 2 3 -0.310 -2.439 -6.805 0.000 0.000 0.000 0.000
[ MATL 1 ]
ML 3 2 3 5 3 -8.003 -0.020 -6.657 -0.389 0.377 -1.236 0.597
D 4 2 3 5 3 -7.923 -3.436 -0.146
IL 5 5 3 5 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
[ MATL 2 ]
ML 6 5 3 8 3 -8.003 -0.020 -6.657 0.711 -1.015 -1.162 0.507
D 7 5 3 8 3 -7.923 -3.436 -0.146
IL 8 8 3 8 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
[ MATL 3 ]
ML 9 8 3 11 3 -8.003 -0.020 -6.657 -0.389 0.377 -1.236 0.597
D 10 8 3 11 3 -7.923 -3.436 -0.146
IL 11 11 3 11 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
[ MATL 4 ]
ML 12 11 3 14 3 -8.003 -0.020 -6.657 -0.392 0.246 -1.238 0.703
D 13 11 3 14 3 -7.923 -3.436 -0.146
IL 14 14 3 14 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
[ MATL 5 ]
ML 15 14 3 17 3 -8.003 -0.020 -6.657 -1.340 -2.411 1.644 -1.777
D 16 14 3 17 3 -7.923 -3.436 -0.146
IL 17 17 3 17 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
[ MATL 6 ]
ML 18 17 3 20 3 -8.003 -0.020 -6.657 0.830 0.106 -1.204 -0.492
D 19 17 3 20 3 -7.923 -3.436 -0.146
IL 20 20 3 20 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
[ MATL 7 ]
ML 21 20 3 23 3 -8.003 -0.020 -6.657 -1.143 -1.575 -1.925 1.560
D 22 20 3 23 3 -7.923 -3.436 -0.146
IL 23 23 3 23 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
[ MATL 8 ]
ML 24 23 3 26 3 -8.391 -0.018 -6.709 0.821 -1.044 -1.178 0.385
D 25 23 3 26 3 -6.905 -0.258 -2.688
IL 26 26 3 26 3 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
[ MATR 9 ]
MR 27 26 3 29 5 -7.411 -0.031 -7.227 -7.439 -8.330 -0.726 0.967 -1.567 0.142
D 28 26 3 29 5 -5.352 -0.707 -2.978 -4.409 -2.404
IR 29 29 3 29 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
[ MATP 10 ]
MP 30 29 3 34 6 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -1.570 -1.865 -1.898 0.327 -1.331 -2.318 0.651 0.994 -1.872 0.282 -2.224 -0.666 1.972 -1.608 -0.242 1.187
ML 31 29 3 34 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.660 -0.612 -0.293 -0.076
MR 32 29 3 34 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.660 -0.612 -0.293 -0.076
D 33 29 3 34 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
IL 34 34 5 34 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
IR 35 35 6 35 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
[ MATP 11 ]
MP 36 35 6 40 4 -7.331 -7.538 -0.041 -5.952 -4.114 0.397 -4.664 0.815 -4.665 -4.015 -0.462 -4.315 -3.939 3.331 -3.732 -0.830 -0.398 -3.640 -1.958 -3.517
ML 37 35 6 40 4 -3.758 -3.940 -0.507 -2.670 0.660 -0.612 -0.293 -0.076
MR 38 35 6 40 4 -4.809 -3.838 -1.706 -0.766 0.660 -0.612 -0.293 -0.076
D 39 35 6 40 4 -4.568 -4.250 -2.265 -0.520
IL 40 40 5 40 4 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
IR 41 41 6 41 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
[ MATL 12 ]
ML 42 41 6 44 5 -7.411 -0.031 -7.227 -7.439 -8.330 1.826 -2.947 -2.856 -2.413
D 43 41 6 44 5 -4.959 -0.803 -4.221 -2.596 -2.508
IL 44 44 3 44 5 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000
[ MATP 13 ]
MP 45 44 3 49 4 -7.331 -7.538 -0.041 -5.952 -1.592 -1.722 -1.807 0.471 -1.387 -2.146 1.822 0.774 -1.836 0.505 -2.076 -0.521 1.055 -1.515 -0.260 0.958
ML 46 44 3 49 4 -3.758 -3.940 -0.507 -2.670 0.660 -0.612 -0.293 -0.076
MR 47 44 3 49 4 -4.809 -3.838 -1.706 -0.766 0.660 -0.612 -0.293 -0.076
D 48 44 3 49 4 -4.568 -4.250 -2.265 -0.520
IL 49 49 5 49 4 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
IR 50 50 6 50 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
[ MATL 14 ]
ML 51 50 6 53 3 -8.323 -0.016 -6.977 0.481 -1.091 -0.011 0.192
D 52 50 6 53 3 -6.174 -1.687 -0.566
IL 53 53 3 53 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
[ MATL 15 ]
ML 54 53 3 56 3 -8.323 -0.016 -6.977 1.148 -1.570 -0.075 -1.007
D 55 53 3 56 3 -6.174 -1.687 -0.566
IL 56 56 3 56 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
[ MATL 16 ]
ML 57 56 3 59 2 * 0.000 -0.726 0.967 -1.567 0.142
D 58 56 3 59 2 * 0.000
IL 59 59 3 59 2 -1.823 -0.479 0.000 0.000 0.000 0.000
[ END 17 ]
E 60 59 3 -1 0
//
"""
CMALIGN_STDOUT = """# cmalign :: align sequences to an RNA CM
# INFERNAL 1.0rc1 (June 2008)
# Copyright 2007-2009 (C) 2008 HHMI Janelia Farm Research Campus
# Freely distributed under the GNU General Public License (GPL)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# command: cmalign --withali aln1.sto -o all_aligned.sto aln1.cm seqs1.fasta
# date: Sun Oct 5 22:04:30 2008
#
# cm name algorithm config sub bands tau
# ------------------------- --------- ------ --- ----- ------
# aln1-1 opt acc global no hmm 1e-07
#
# bit scores
# ------------------
# seq idx seq name len total struct avg prob elapsed
# ------- -------- ----- -------- -------- -------- -----------
1 1 23 -9.98 5.71 0.260 00:00:00.01
2 2 13 -6.79 6.73 0.710 00:00:00.00
3 3 17 -7.43 5.86 0.754 00:00:00.01
# Alignment saved in file all_aligned.sto.
#
# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00
"""
if __name__ == '__main__':
main()
