#!/usr/bin/env python
from cogent.app.util import CommandLineApplication,\
CommandLineAppResult, ResultPath
from cogent.app.parameters import Parameter, FlagParameter, ValuedParameter,\
MixedParameter,Parameters, _find_synonym, is_not_None
from cogent.struct.rna2d import ViennaStructure
from cogent.core.alignment import DataError
from cogent.parse.rnaalifold import MinimalRnaalifoldParser
from random import choice
__author__ = "Rob Knight"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Jeremy Widmann", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Sandra Smit"
__email__ = "Sandra.Smit@colorado.edu"
__status__ = "Production"
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
def get_constrained_fold(sequence, constraint_string, params=None):
"""Returns secondary structure from RNAfold with constraints.
- sequence: RNA sequence object or string.
- constraint_string: RNAfold folding constraint string.
- params: dict of additional RNAfold parameters.
"""
#Check that sequence and constraint string exist.
if not sequence:
raise ValueError, 'No sequence found!'
elif not constraint_string:
raise ValueError, 'No constraint string found!'
sequence = str(sequence)
#Check that sequence and constraint_string are equal length.
if len(sequence) != len(constraint_string):
raise ValueError, 'Sequence and constraint string are not same length!'
app = RNAfold(params=params)
#Turn on constrained folding.
app.Parameters['-C'].on()
res = app([sequence,constraint_string])
#Parse out seq, struct string and energy.
seq, struct, energy = MinimalRnaalifoldParser(res['StdOut'].readlines())[0]
#Clean up after application.
res.cleanUp()
return seq, struct, energy
def get_secondary_structure(sequence, params=None):
"""Returns secondary structure from RNAfold.
- sequence: RNA sequence object or string.
- params: dict of additional RNAfold parameters.
"""
#Check that sequence and constraint string exist.
if not sequence:
raise ValueError, 'No sequence found!'
sequence = str(sequence)
app = RNAfold(params=params)
res = app([sequence])
#Parse out seq, struct string and energy.
seq, struct, energy = MinimalRnaalifoldParser(res['StdOut'].readlines())[0]
#Clean up after application.
res.cleanUp()
return seq, struct, energy
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))])
class RNAplot(CommandLineApplication):
"""Application controller for RNAplot (in the Vienna RNA package)
Manual on:
http://www.tbi.univie.ac.at/~ivo/RNA/RNAplot.html
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 = {
#-t 0|1 Choose the layout algorithm. Simple radial layout if 0, or
# naview if 1. Default is 1.
'-t':ValuedParameter(Prefix='-',Name='t',Delimiter=' '),\
#-o ps|gml|xrna|svg
# Specify output format. Available formats are: PostScript (ps),
# Graph Meta Language (gml), Scalable Vector Graphics (svg), and
# XRNA save file (xrna). Output filenames will end in ".ps" ".gml"
# ".svg" ".ss", respectively. Default is ps.
'-o':ValuedParameter(Prefix='-',Name='o',Delimiter=' '),\
#--pre string --post string
# Add annotation macros to postscript file, and add the postscript
# code in "string" just before (--pre) or after (--post) the code
# to draw the structure. This is an easy way to add annotation,
# e.g to mark position 15 with circle use --post "15 cmark"
'--pre':ValuedParameter(Prefix='--',Name='pre',Delimiter=' '),\
'--post':ValuedParameter(Prefix='--',Name='post',Delimiter=' '),\
}
_command = 'RNAplot'
_input_handler = '_input_as_lines'
_suppress_stderr = True
FILETYPE_TO_EXTENSION = {'ps':'.ps',\
'gml':'.gml',\
'svg':'.svg',\
'xrna':'.ss'
}
def getHelp(self):
"""Method that points to the RNAplot documentation."""
help_str = \
"""
See RNAplot documentation at:
http://www.tbi.univie.ac.at/~ivo/RNA/RNAplot.html
"""
return help_str
def _get_tmp_seqname(self):
"""Returns a temporary name for sequence.
- Useful since RNAplot names plot files according to sequence
name when available. Will use the 'rna' prefix if no
sequence name is supplied.
- Note only takes first 12 characters as the name. So this function
will only use make a name 9 long with 'tmp' as a prefix.
"""
chars = "abcdefghigklmnopqrstuvwxyz"
picks = chars + chars.upper() + "0123456790"
return 'tmp'+''.join([choice(picks) for i in range(9)])
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(RNAplot,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(RNAplot,self)._input_as_lines(data))])
def _get_outfile_extension(self):
"""Returns file extension of RNAplot.
"""
if not self.Parameters['-o'].isOn():
return '.ps'
else:
filetype = self._absolute(str(self.Parameters['-o'].Value))
return self.FILETYPE_TO_EXTENSION[filetype]
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
RNAplot can produce one output files:
a secondary structure structure graph.
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 files for
named sequences will be written to name_ss.ps.
"""
result = {}
name_counter = 0
seq_counter = 0
if not isinstance(data,list):
#means data is file
data = open(data).readlines()
res_extension = self._get_outfile_extension()
for item in data:
if item.startswith('>'):
name_counter += 1
name = item.strip('>\n')
result[(name+'_ss')] =\
ResultPath(Path=(self.WorkingDir+name+'_ss'+res_extension))
else:
seq_counter += 1
if (seq_counter/2 - name_counter > 0):
result['SS'] = ResultPath(Path=self.WorkingDir+'rna'+res_extension,\
IsWritten=True) #Secondary Structure
return result
def plot_from_seq_and_struct(seq, struct,seqname=None, params=None):
"""Returns plot of structure given seq and struct.
- seq: sequence corresponding to struct.
- Can be anything that behaves as a string same length as struct.
- struct: Vienna structure corresponding to seq. Must be a valid
Vienna structure.
"""
seq = str(seq)
#Construct ViennaStructure. Object will handle errors in struct string.
struct = ViennaStructure(struct)
if len(seq) != len(struct):
raise DataError, 'Sequence and structure are not same length!'
app = RNAplot(WorkingDir='/tmp',\
params=params)
if seqname is None:
seqname = app._get_tmp_seqname()
res = app(['>'+seqname,seq,struct])
plot = res[seqname+'_ss'].read()
res.cleanUp()
return plot
