def test_str_all_modes(self):
"""MixedParameter: str() functions in various modes """
p = MixedParameter(Prefix='-',Name='d',Delimiter='=',Quote=']')
self.assertEqual(str(p),'')
p.on()
self.assertEqual(str(p),'-d')
p.on('a')
self.assertEqual(str(p),'-d=]a]')
class RNAsubopt(CommandLineApplication):
"""Application controller for RNAsubopt (in the Vienna RNA package)
Manual on:
http://www.tbi.univie.ac.at/~ivo/RNA/RNAsubopt.html
http://bioweb.pasteur.fr/docs/man/man/RNAsubopt.1.html
Parameters with default values:
-e: 1 (range)
-T: 37 (temperature)
-d: 2 (dangling ends as in partition function folding)
Input is always written to a file which is used as the application's input.
StdErr is suppressed by default, but can be overwritten in an instance.
"""
_parameters = {
'-p': ValuedParameter(Prefix='-', Name='p', Delimiter=' '),
'-C': FlagParameter(Prefix='-', Name='C'),
'-e': ValuedParameter(Prefix='-', Name='e', Delimiter=' ', Value=1),
'-ep': ValuedParameter(Prefix='-', Name='ep', Delimiter=' '),
'-s': FlagParameter(Prefix='-', Name='s'),
'-lodos': FlagParameter(Prefix='-', Name='lodos'),
'-T': ValuedParameter(Prefix='-', Name='T', Value=37, Delimiter=' '),
'-4': FlagParameter(Prefix='-', Name=4),
'-d': MixedParameter(Prefix='-', Name='d', Delimiter='', Value=2),
'-noGU': FlagParameter(Prefix='-', Name='noGU'),
'-noCloseGU': FlagParameter(Prefix='-', Name='noCloseGU'),
'-P': ValuedParameter(Prefix='-', Name='P', Delimiter=' '),
'-logML': FlagParameter(Prefix='-', Name='logML'),
'-nsp': ValuedParameter(Prefix='-', Name='nsp', Delimiter=' '),
'-noLP': FlagParameter(Prefix='-', Name='noLP')
}
_synonyms = {
'Temperature': '-T',
'Temp': '-T',
'EnergyRange': '-e',
'Sort': '-s'
}
_command = 'RNAsubopt'
_input_handler = '_input_as_lines'
_suppress_stderr = True
def _input_as_path(self, filename):
"""Returns '>"filename"' to redirect input to stdin
Includes quotes to handle file names containing spaces.
"""
return ''.join(\
['<',str(super(RNAsubopt,self)._input_as_path(filename))])
def _input_as_lines(self, data):
"""Returns '>temp_filename to redirect input to stdin
Includes quotes to handle file names containing spaces.
"""
return ''.join(
['<', str(super(RNAsubopt, self)._input_as_lines(data))])
def setUp(self):
self.fp = FlagParameter(Prefix='-', Name='d')
self.vp = ValuedParameter(Name='p', Prefix='-', Value=[1])
self.mp = MixedParameter(Prefix='--', Name='k', Delimiter=' ')
self.all_params = {
self.fp.Id: self.fp,
self.vp.Id: self.vp,
self.mp.Id: self.mp
}
self.p1 = Parameters()
self.p2 = Parameters(self.all_params)
self._synonyms = {'Pino': '-p', 'K': 'k'}
self.p3 = Parameters(self.all_params, self._synonyms)
def test_str_all_modes(self):
"""MixedParameter: str() functions in various modes """
p = MixedParameter(Prefix='-', Name='d', Delimiter='=', Quote=']')
self.assertEqual(str(p), '')
p.on()
self.assertEqual(str(p), '-d')
p.on('a')
self.assertEqual(str(p), '-d=]a]')
class RNAfold(CommandLineApplication):
"""Application controller for RNAfold (in the Vienna RNA package)
Manual on:
http://www.tbi.univie.ac.at/~ivo/RNA/RNAfold.html
http://bioweb.pasteur.fr/docs/man/man/RNAfold.1.html
Parameters with default values:
-T: 37 (temperature)
-d: 1 (only unpaired bases in dangling ends)
-S: 1.07 (scale)
Input is always written to a file which is used as the application's input.
StdErr is suppressed by default, but can be overruled in an instance.
"""
_parameters = {
'-p':MixedParameter(Prefix='-',Name='p',Delimiter='',Value=False),
'-C':FlagParameter(Prefix='-',Name='C'),
'-T':ValuedParameter(Prefix='-',Name='T',Value=37,Delimiter=' '),
'-4':FlagParameter(Prefix='-',Name=4),
'-d':MixedParameter(Prefix='-',Name='d',Delimiter='',Value=1),
'-noLP':FlagParameter(Prefix='-',Name='noLP'),
'-noGU':FlagParameter(Prefix='-',Name='noGU'),
'-noCloseGU':FlagParameter(Prefix='-',Name='noCloseGU'),
'-e':ValuedParameter(Prefix='-',Name='e',Delimiter=' '),
'-P':ValuedParameter(Prefix='-',Name='P',Delimiter=' '),
'-nsp':ValuedParameter(Prefix='-',Name='nsp',Delimiter=' '),
'-S':ValuedParameter(Prefix='-',Name='S',Value=1.07,Delimiter=' ')}
_synonyms = {'Temperature':'-T','Temp':'-T','Scale':'-S'}
_command = 'RNAfold'
_input_handler = '_input_as_lines'
_suppress_stderr = True
def _input_as_path(self,filename):
"""Returns '>"filename"' to redirect input to stdin"""
return ''.join(\
['<', str(super(RNAfold,self)._input_as_path(filename))])
def _input_as_lines(self,data):
"""Returns '>"temp_filename" to redirect input to stdin"""
return ''.join(['<',str(super(RNAfold,self)._input_as_lines(data))])
def _get_result_paths(self,data):
"""Specifies the paths of output files generated by the application
data: the data the instance of the application is called on
You always get back: StdOut,StdErr, and ExitStatus
RNAfold can produce two additional output files:
a secondary structure structure graph. Default name: rna.ps
a dot plot of the base pairing matrix. Default name: dp.ps
The default names are used for unnamed sequences. Files are created
in the current working directory.
You can make a sequence named by inserting a line '>name' above it in
your input file (or list of sequences). The ss and dp files for
named sequences will be written to name_ss.ps and name_dp.ps
"""
result = {}
name_counter = 0
seq_counter = 0
if not isinstance(data,list):
#means data is file
data = open(data).readlines()
for item in data:
if item.startswith('>'):
name_counter += 1
name = item.strip('>\n')
result[(name+'_ss')] =\
ResultPath(Path=(self.WorkingDir+name+'_ss.ps'))
result[(name+'_dp')] =\
ResultPath(Path=(self.WorkingDir+name+'_dp.ps'),\
IsWritten=self.Parameters['-p'].isOn())
else:
seq_counter += 1
result['SS'] = ResultPath(Path=self.WorkingDir+'rna.ps',\
IsWritten=seq_counter - name_counter > 0) #Secondary Structure
result['DP'] = ResultPath(Path=self.WorkingDir+'dot.ps',
IsWritten=(self.Parameters['-p'].isOn() and\
seq_counter - name_counter > 0)) #DotPlot
return result
class Clustalw(CommandLineApplication):
""" clustalw application controller
The parameters are organized by function to give some idea of how the
program works. However, no restrictions are put on any combinations
of parameters. Misuse of parameters can lead to errors or otherwise
strange results.
You are supposed to choose one action for the program to perform. (align,
profile, sequences, tree, or bootstrap). If you choose multiple, only the
dominant action (see order above) will be executed. By DEFAULT, the -align
parameter is turned on. If you decide to turn another one on, you should
turn '-align' off IN ADDITION!
Some references to help pages are available in the 'getHelp' method.
Some might be useful to you.
"""
_actions = {\
'-align':FlagParameter('-','align',Value=True),
'-profile':FlagParameter('-','profile'),
'-sequences':FlagParameter('-','sequences'),
'-tree':FlagParameter('-','tree'),
'-bootstrap':MixedParameter('-','bootstrap',Delimiter='=')}
#sequence file for alignment, or alignment file for bootstrap and tree
#actions
_input = {
'-infile': ValuedParameter('-', 'infile', Delimiter='=', IsPath=True)
}
# matrix and dnamatrix can be filenames as well, but not always.
# They won't be treated as filenames and thus not quoted.
# Therefore filepaths containing spaces might result in errors.
_multiple_alignment={\
'-quicktree':FlagParameter('-','quicktree'),
'-type':ValuedParameter('-','type',Delimiter='='),
'-matrix':ValuedParameter('-','matrix',Delimiter='='),
'-dnamatrix':ValuedParameter('-','dnamatrix',Delimiter='='),
'-gapopen':ValuedParameter('-','gapopen',Delimiter='='),
'-gapext':ValuedParameter('-','gapext',Delimiter='='),
'-endgaps':FlagParameter('-','endgaps'),
'-gapdist':ValuedParameter('-',Name='gapdist',Delimiter='='),
'-nopgap':FlagParameter('-','nopgap'),
'-nohgap':FlagParameter('-','nohgap'),
'-hgapresidues':ValuedParameter('-','hgapresidues',Delimiter='='),
'-maxdiv':ValuedParameter('-',Name='maxdiv',Delimiter='='),
'-negative':FlagParameter('-','negative'),
'-transweight':ValuedParameter('-',Name='transweight',Delimiter='='),
'-newtree':ValuedParameter('-','newtree',Delimiter='=',IsPath=True),
'-usetree':ValuedParameter('-','usetree',Delimiter='=',IsPath=True)}
_fast_pairwise={\
'-ktuple':ValuedParameter('-',Name='ktuple',Delimiter='='),
'-topdiags':ValuedParameter('-',Name='topdiags',Delimiter='='),
'-window':ValuedParameter('-',Name='window',Delimiter='='),
'-pairgap':ValuedParameter('-',Name='pairgap',Delimiter='='),
'-score':ValuedParameter('-',Name='score',Delimiter='=')}
# pwmatrix and pwdnamatrix can be filenames as well, but not always.
# They won't be treated as filenames and thus not quoted.
# Therefore filepaths containing spaces might result in errors.
_slow_pairwise={\
'-pwmatrix':ValuedParameter('-',Name='pwmatrix',Delimiter='='),
'-pwdnamatrix':ValuedParameter('-',Name='pwdnamatrix',Delimiter='='),
'-pwgapopen':ValuedParameter('-',Name='pwgapopen',Delimiter='='),
'-pwgapext':ValuedParameter('-',Name='pwgapext',Delimiter='=')}
#plus -bootstrap
_tree={\
'-kimura':FlagParameter('-',Name='kimura'),
'-tossgaps':FlagParameter('-',Name='tossgaps'),
'-bootlabels':ValuedParameter('-',Name='bootlabels',Delimiter='='),
'-seed':ValuedParameter('-',Name='seed',Delimiter='='),
'-outputtree':ValuedParameter('-',Name='outputtree',Delimiter='=')}
_output={\
'-outfile':ValuedParameter('-',Name='outfile',Delimiter='=',\
IsPath=True),
'-output':ValuedParameter('-',Name='output',Delimiter='='),
'-case':ValuedParameter('-',Name='case',Delimiter='='),
'-outorder':ValuedParameter('-',Name='outorder',Delimiter='='),
'-seqnos':ValuedParameter('-',Name='seqnos',Delimiter='=')}
_profile_alignment={\
'-profile1':ValuedParameter('-','profile1',Delimiter='=',IsPath=True),
'-profile2':ValuedParameter('-','profile2',Delimiter='=',IsPath=True),
'-usetree1':ValuedParameter('-','usetree1',Delimiter='=',IsPath=True),
'-usetree2':ValuedParameter('-','usetree2',Delimiter='=',IsPath=True),
'-newtree1':ValuedParameter('-','newtree1',Delimiter='=',IsPath=True),
'-newtree2':ValuedParameter('-','newtree2',Delimiter='=',IsPath=True)}
_structure_alignment={\
'-nosecstr1':FlagParameter('-',Name='nosecstr1'),
'-nosecstr2':FlagParameter('-',Name='nosecstr2'),
'-helixgap':ValuedParameter('-',Name='helixgap',Delimiter='='),
'-strandgap':ValuedParameter('-',Name='strandgap',Delimiter='='),
'-loopgap':ValuedParameter('-',Name='loopgap',Delimiter='='),
'-terminalgap':ValuedParameter('-',Name='terminalgap',Delimiter='='),
'-helixendin':ValuedParameter('-',Name='helixendin',Delimiter='='),
'-helixendout':ValuedParameter('-',Name='helixendout',Delimiter='='),
'-strandendin':ValuedParameter('-',Name='strandendin',Delimiter='='),
'-strandendout':ValuedParameter('-',Name='strandendout',Delimiter='='),
'-secstrout':ValuedParameter('-',Name='secstrout',Delimiter='=')}
#NOT SUPPORTED
#'-help':FlagParameter('-','help'),
#'-check':FlagParameter('-','check'),
#'-options':FlagParameter('-','options'),
#'-convert':FlagParameter('-','convert'),
#'-batch':FlagParameter('-','batch'),
#'-noweights':FlagParameter('-','noweights'),
#'-novgap':FlagParameter('-','novgap'),
#'-debug':ValuedParameter('-',Name='debug',Delimiter='='),
_parameters = {}
_parameters.update(_actions)
_parameters.update(_input)
_parameters.update(_multiple_alignment)
_parameters.update(_fast_pairwise)
_parameters.update(_slow_pairwise)
_parameters.update(_tree)
_parameters.update(_output)
_parameters.update(_profile_alignment)
_parameters.update(_structure_alignment)
_command = 'clustalw'
def getHelp(self):
"""Methods that points to the documentation"""
help_str =\
"""
There are several help pages available online. For example:
http://searchlauncher.bcm.tmc.edu/multi-align/Help/
clustalw_help_1.8.html
http://hypernig.nig.ac.jp/homology/clustalw-e_help.html
http://www.genebee.msu.su/clustal/help.html
A page that give reasonable insight in use of the parameters:
http://bioweb.pasteur.fr/seqanal/interfaces/clustalw.html
"""
return help_str
def _input_as_multiline_string(self, data):
"""Writes data to tempfile and sets -infile parameter
data -- list of lines
"""
if data:
self.Parameters['-infile']\
.on(super(Clustalw,self)._input_as_multiline_string(data))
return ''
def _input_as_lines(self, data):
"""Writes data to tempfile and sets -infile parameter
data -- list of lines, ready to be written to file
"""
if data:
self.Parameters['-infile']\
.on(super(Clustalw,self)._input_as_lines(data))
return ''
def _input_as_seqs(self, data):
"""writes sequences to tempfile and sets -infile parameter
data -- list of sequences
Adds numbering to the sequences: >1, >2, etc.
"""
lines = []
for i, s in enumerate(data):
#will number the sequences 1,2,3,etc.
lines.append(''.join(['>', str(i + 1)]))
lines.append(s)
return self._input_as_lines(lines)
def _input_as_string(self, data):
"""Makes data the value of a specific parameter
This method returns the empty string. The parameter will be printed
automatically once set.
"""
if data:
self.Parameters['-infile'].on(data)
return ''
def _suffix(self):
"""Return appropriate suffix for alignment file"""
_output_formats = {
'GCG': '.msf',
'GDE': '.gde',
'PHYLIP': '.phy',
'PIR': '.pir',
'NEXUS': '.nxs'
}
if self.Parameters['-output'].isOn():
return _output_formats[self.Parameters['-output'].Value]
else:
return '.aln'
def _aln_filename(self, prefix):
"""Return name of file containing the alignment
prefix -- str, prefix of alignment file.
"""
if self.Parameters['-outfile'].isOn():
aln_filename = self._absolute(self.Parameters['-outfile'].Value)
else:
aln_filename = prefix + self._suffix()
return aln_filename
def _tempfile_as_multiline_string(self, data):
"""Write a multiline string to a temp file and return the filename.
data: a multiline string to be written to a file.
* Note: the result will be the filename as a FilePath object
(which is a string subclass).
"""
filename = FilePath(self.getTmpFilename(self.TmpDir))
data_file = open(filename, 'w')
data_file.write(data)
data_file.close()
return filename
def _get_result_paths(self, data):
"""Return dict of {key: ResultPath}
"""
#clustalw .aln is used when no or unkown output type specified
_treeinfo_formats = {'nj': '.nj', 'dist': '.dst', 'nexus': '.tre'}
result = {}
par = self.Parameters
abs = self._absolute
if par['-align'].isOn():
prefix = par['-infile'].Value.rsplit('.', 1)[0]
#prefix = par['-infile'].Value.split('.')[0]
aln_filename = self._aln_filename(prefix)
if par['-newtree'].isOn():
dnd_filename = abs(par['-newtree'].Value)
elif par['-usetree'].isOn():
dnd_filename = abs(par['-usetree'].Value)
else:
dnd_filename = abs(prefix + '.dnd')
result['Align'] = ResultPath(Path=aln_filename, IsWritten=True)
result['Dendro'] = ResultPath(Path=dnd_filename, IsWritten=True)
elif par['-profile'].isOn():
prefix1 = par['-profile1'].Value.rsplit('.', 1)[0]
prefix2 = par['-profile2'].Value.rsplit('.', 1)[0]
#prefix1 = par['-profile1'].Value.split('.')[0]
#prefix2 = par['-profile2'].Value.split('.')[0]
aln_filename = ''
aln_written = True
dnd1_filename = ''
tree1_written = True
dnd2_filename = ''
tree2_written = True
aln_filename = self._aln_filename(prefix1)
#usetree1
if par['-usetree1'].isOn():
tree1_written = False
#usetree2
if par['-usetree2'].isOn():
tree2_written = False
if par['-newtree1'].isOn():
dnd1_filename = abs(par['-newtree1'].Value)
aln_written = False
else:
dnd1_filename = abs(prefix1 + '.dnd')
if par['-newtree2'].isOn():
dnd2_filename = abs(par['-newtree2'].Value)
aln_written = False
else:
dnd2_filename = abs(prefix2 + '.dnd')
result['Align'] = ResultPath(Path=aln_filename,
IsWritten=aln_written)
result['Dendro1'] = ResultPath(Path=dnd1_filename,
IsWritten=tree1_written)
result['Dendro2'] = ResultPath(Path=dnd2_filename,
IsWritten=tree2_written)
elif par['-sequences'].isOn():
prefix1 = par['-profile1'].Value.rsplit('.', 1)[0]
prefix2 = par['-profile2'].Value.rsplit('.', 1)[0]
#prefix1 = par['-profile1'].Value.split('.')[0] #alignment
#prefix2 = par['-profile2'].Value.split('.')[0] #sequences
aln_filename = ''
aln_written = True
dnd_filename = ''
dnd_written = True
aln_filename = self._aln_filename(prefix2)
if par['-usetree'].isOn():
dnd_written = False
elif par['-newtree'].isOn():
aln_written = False
dnd_filename = abs(par['-newtree'].Value)
else:
dnd_filename = prefix2 + '.dnd'
result['Align'] = ResultPath(Path=aln_filename,\
IsWritten=aln_written)
result['Dendro'] = ResultPath(Path=dnd_filename,\
IsWritten=dnd_written)
elif par['-tree'].isOn():
prefix = par['-infile'].Value.rsplit('.', 1)[0]
#prefix = par['-infile'].Value.split('.')[0]
tree_filename = ''
tree_written = True
treeinfo_filename = ''
treeinfo_written = False
tree_filename = prefix + '.ph'
if par['-outputtree'].isOn() and\
par['-outputtree'].Value != 'phylip':
treeinfo_filename = prefix +\
_treeinfo_formats[par['-outputtree'].Value]
treeinfo_written = True
result['Tree'] = ResultPath(Path=tree_filename,\
IsWritten=tree_written)
result['TreeInfo'] = ResultPath(Path=treeinfo_filename,\
IsWritten=treeinfo_written)
elif par['-bootstrap'].isOn():
prefix = par['-infile'].Value.rsplit('.', 1)[0]
#prefix = par['-infile'].Value.split('.')[0]
boottree_filename = prefix + '.phb'
result['Tree'] = ResultPath(Path=boottree_filename, IsWritten=True)
return result
class FastTree(CommandLineApplication):
"""FastTree application Controller"""
_command = 'FastTree'
_input_handler = '_input_as_multiline_string'
_parameters = {
'-quiet':FlagParameter('-',Name='quiet'),
'-boot':ValuedParameter('-',Delimiter=' ',Name='boot'),
'-seed':ValuedParameter('-',Delimiter=' ',Name='seed'),
'-nni':ValuedParameter('-',Delimiter=' ',Name='nni'),
'-slow':FlagParameter('-',Name='slow'),
'-fastest':FlagParameter('-',Name='fastest'),
'-top':FlagParameter('-',Name='top'),
'-notop':FlagParameter('-',Name='notop'),
'-topm':ValuedParameter('-',Delimiter=' ',Name='topm'),
'-close':ValuedParameter('-',Delimiter=' ',Name='close'),
'-refresh':ValuedParameter('-',Delimiter=' ',Name='refresh'),
'-matrix':ValuedParameter('-',Delimiter=' ',Name='matrix'),
'-nomatrix':FlagParameter('-',Name='nomatrix'),
'-nj':FlagParameter('-',Name='nj'),
'-bionj':FlagParameter('-',Name='bionj'),
'-nt':FlagParameter('-',Name='nt'),
'-n':ValuedParameter('-',Delimiter=' ',Name='n'),
'-pseudo':MixedParameter('-',Delimiter=' ', Name='pseudo'),
'-intree':ValuedParameter('-',Delimiter=' ',Name='intree'),
'-spr':ValuedParameter('-',Delimiter=' ',Name='spr'),
'-constraints':ValuedParameter('-',Delimiter=' ',\
Name='constraints'),
'-constraintWeight':ValuedParameter('-',Delimiter=' ',\
Name='constraintWeight'),\
'-makematrix':ValuedParameter('-',Delimiter=' ',Name='makematrix')}
def __call__(self, data=None, remove_tmp=True):
"""Run the application with the specified kwargs on data
data: anything that can be cast into a string or written out to
a file. Usually either a list of things or a single string or
number. input_handler will be called on this data before it
is passed as part of the command-line argument, so by creating
your own input handlers you can customize what kind of data
you want your application to accept
remove_tmp: if True, removes tmp files
NOTE: Override of the base class to handle redirected output
"""
input_handler = self.InputHandler
suppress_stderr = self.SuppressStderr
outfile = self.getTmpFilename(self.TmpDir)
self._outfile = outfile
if suppress_stderr:
errfile = FilePath('/dev/null')
else:
errfile = FilePath(self.getTmpFilename(self.TmpDir))
if data is None:
input_arg = ''
else:
input_arg = getattr(self, input_handler)(data)
# Build up the command, consisting of a BaseCommand followed by
# input and output (file) specifications
command = self._command_delimiter.join(filter(None,\
[self.BaseCommand,str(input_arg),'>',str(outfile),'2>',\
str(errfile)]))
if self.HaltExec:
raise AssertionError, "Halted exec with command:\n" + command
# The return value of system is a 16-bit number containing the signal
# number that killed the process, and then the exit status.
# We only want to keep the exit status so do a right bitwise shift to
# get rid of the signal number byte
exit_status = system(command) >> 8
# Determine if error should be raised due to exit status of
# appliciation
if not self._accept_exit_status(exit_status):
raise ApplicationError, \
'Unacceptable application exit status: %s, command: %s'\
% (str(exit_status),command)
out = open(outfile, "r")
err = None
if not suppress_stderr:
err = open(errfile, "r")
result = CommandLineAppResult(out,err,exit_status,\
result_paths=self._get_result_paths(data))
# Clean up the input file if one was created
if remove_tmp:
if self._input_filename:
remove(self._input_filename)
self._input_filename = None
return result
def _get_result_paths(self, data):
result = {}
result['Tree'] = ResultPath(Path=self._outfile)
return result
class RNAalifold(CommandLineApplication):
"""Application controller for RNAalifold application
reads aligned RNA sequences from stdin or file.aln and calculates
their minimum free energy (mfe) structure, partition function
(pf) and base pairing probability matrix.
OPTIONS
-cv <float>
Set the weight of the covariance term in the energy function to
factor. Default is 1.
-nc <float>
Set the penalty for non-compatible sequences in the covariance
term of the energy function to factor. Default is 1.
-E Score pairs with endgaps same as gap-gap pairs.
-mis Output \"most informative sequence\" instead of simple consensus:
For each column of the alignment output the set of nucleotides
with frequence greater than average in IUPAC notation.
-p Calculate the partition function and base pairing probability
matrix in addition to the mfe structure. Default is calculation
of mfe structure only.
-noLP Avoid structures without lonely pairs (helices of length 1). In
the mfe case structures with lonely pairs are strictly forbid-
den. For partition function folding this disallows pairs that
can only occur isolated. Setting this option provides a signif-
icant speedup.
The -T, -d, -4, -noGU, -noCloseGU, -e, -P, -nsp, options should work as
in RNAfold
If using -C constraints will be read from stdin, the alignment has to
given as a filename on the command line.
For more info see respective man pages.
"""
_parameters = {
'-cv': ValuedParameter(Prefix='-', Name='cv', Delimiter=' '),
'-nc': ValuedParameter(Prefix='-', Name='nc', Delimiter=' '),
'-E': FlagParameter(Prefix='-', Name='E'),
'-mis': FlagParameter(Prefix='-', Name='mis'),
'-noLP': FlagParameter(Prefix='-', Name='noLP'),
'-T': ValuedParameter(Prefix='-', Name='T', Value=37, Delimiter=' '),
'-4': FlagParameter(Prefix='-', Name=4),
'-d': MixedParameter(Prefix='-', Name='d', Delimiter=''),
'-noGU': FlagParameter(Prefix='-', Name='noGU'),
'-noCloseGU': FlagParameter(Prefix='-', Name='noCloseGU'),
'-e': ValuedParameter(Prefix='-', Name='e', Delimiter=' '),
'-P': ValuedParameter(Prefix='-', Name='P', Delimiter=' '),
'-nsp': ValuedParameter(Prefix='-', Name='nsp', Delimiter=' '),
'-C': FlagParameter(Prefix='-', Name='C')
}
_synonyms = {'Temperature': '-T', 'Temp': '-T', 'EnergyRange': '-e'}
_command = 'RNAalifold'
_input_handler = '_input_as_string'
def _get_result_paths(self, data):
"""Specify the paths of the output files generated by the application
You always get back: StdOut, StdErr, and ExitStatus.
In addition RNAalifold writes a file: alirna.ps. It seems that this
file is always written (no exceptions found so far.
The documentation says the application can produce a dotplot
(alidot.ps), but it is unclear when this file is produced, and
thus it is not added to the results dictionary.
"""
result = {}
result['SS'] = ResultPath(Path=self.WorkingDir+'alirna.ps',\
IsWritten=True)
return result