#!/usr/bin/env python from cogent.app.util import CommandLineApplication,\ CommandLineAppResult, ResultPath, ApplicationError from cogent.app.parameters import Parameter, FlagParameter, ValuedParameter,\ MixedParameter,Parameters from sys import platform from os import remove,system,mkdir,getcwd,close __author__ = "Shandy Wikman" __copyright__ = "Copyright 2007-2016, The Cogent Project" __contributors__ = ["Shandy Wikman", "Daniel McDonald"] __license__ = "GPL" __version__ = "1.9" __maintainer__ = "Shandy Wikman" __email__ = "ens01svn@cs.umu.se" __status__ = "Development" class Dynalign(CommandLineApplication): """Application controller for Dynalign Input: Sequences for input in Dynalign are assumed to be in the following format: ;(first line of file) Comments must start with a ;semicolon ;There can be any number of comments A single line title must immediately follow: AAA GCGG UUTGTT UTCUTaaTCTXXXXUCAGG1 where the terminal 1 is required at the end. pknotsRG is a tool for thermodynamic folding of RNA secondary structures, including the class of canonical simple recursive pseudoknots. -alignment The alignment file that will be created -M Maximum seperation parameter (larger then diff in length of seq) -gap_cost 0.4 good value -max_precent_diff maximum % diff in free energy in suboptimal struct. 20 good starting point -bp_window specifies how different the suboptimal structures must be from each other. 2 good starting point -align_window specifies how different alignments must be, 1 good starting point. -single_bp_inserts specifies whether single base pair inserts are allowed; 0 = no; 1 = yes. -[savefile] optional """ _parameters = { '-alignment':ValuedParameter(Prefix='',Name='',Value='align',Delimiter=' '), '-M':ValuedParameter(Prefix='',Name='',Value=10,Delimiter=' '), '-gap_cost':ValuedParameter(Prefix='',Name='',Value=0.4,Delimiter=' '), '-max_structures':ValuedParameter(Prefix='',Name='',Value=8,Delimiter=' '), '-max_percent_diff':ValuedParameter(Prefix='',Name='',Value=20,\ Delimiter=' '), '-bp_window':ValuedParameter(Prefix='',Name='',Value=2,Delimiter=' '), '-align_window':ValuedParameter(Prefix='',Name='',Value=1,Delimiter=' '), '-single_bp_inserts':ValuedParameter(Prefix='',Name='',Value=1,\ Delimiter=' '),} _command = 'dynalign' _input_handler = '_input_as_string' def _input_as_string(self,data): """Return data as a string Data = list with two file paths ex: data = ['path1,'path2'']""" inputFiles = '' self._input_filename = [] for i in data: self._input_filename.append(i) inputFiles = ' '.join([inputFiles,i]) outputFile = ' '.join(['ct1', 'ct2']) inputFiles = ' '.join([inputFiles,outputFile]) return inputFiles def _input_as_lines(self,data): """ Write a seq of lines to a temp file and return the filename string data: a sequence to be written to a file, each element of the sequence will compose a line in the file. ex. data = [file1,file2], file1 and 2 is lists of lines -> [[List],[List]] Note: '\n' will be stripped off the end of each sequence element before writing to a file in order to avoid multiple new lines accidentally be written to a file """ inputFiles = '' self._input_filename = [] for el in data: filename = self.getTmpFilename(self.WorkingDir) self._input_filename.append(filename) data_file = open(filename,'w') data_to_file = '\n'.join([str(d).strip('\n') for d in el]) data_file.write(data_to_file) data_file.close() inputFiles = ' '.join([inputFiles,filename]) outputFiles = ' '.join(['ct1', 'ct2']) inputFiles = ' '.join([inputFiles,outputFiles]) return inputFiles def _get_result_paths(self,data): """ data: the data the instance of the application is called on """ result = {} result['seq_1_ct'] =\ ResultPath(Path=(self.WorkingDir+'ct1')) result['seq_2_ct'] =\ ResultPath(Path=(self.WorkingDir+'ct2')) result['alignment'] =\ ResultPath(Path=(self.WorkingDir+'align')) return result #Below from Cogent/app/util.py modified to accommodate dynalign def __call__(self,data=None): """Run the application with the specified kwargs on data Overides the __call__ function in util.py becasue of the special circumstance surrounding the command line input. 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 you application to accept """ input_handler = self.InputHandler suppress_stdout = self.SuppressStdout suppress_stderr = self.SuppressStderr if suppress_stdout: outfile = '/dev/null' else: outfile = self.getTmpFilename(self.WorkingDir) if suppress_stderr: errfile = '/dev/null' else: errfile = self.getTmpFilename(self.WorkingDir) 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 first,second=self.BaseCommand command = self._command_delimiter.join(filter(None,\ [first,input_arg,second,'>',outfile,'2>',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) # open the stdout and stderr if not being suppressed out = None if not suppress_stdout: 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 self._input_filename: for f in self._input_filename: remove(f) self._input_filename = None return result def _get_base_command(self): """ Returns the full command string Overides the __call__ function in util.py becasue of the special circumstance surrounding the command line input. input_arg: the argument to the command which represents the input to the program, this will be a string, either representing input or a filename to get input from """ command_part1 = [] command_part2 = [] # Append a change directory to the beginning of the command to change # to self.WorkingDir before running the command cd_command = ''.join(['cd ',self.WorkingDir,';']) if self._command is None: raise ApplicationError, '_command has not been set.' command = self._command command_part1.append(cd_command) command_part1.append(command) lista = [self.Parameters['-alignment'],\ self.Parameters['-M'],\ self.Parameters['-gap_cost'],\ self.Parameters['-max_structures'],\ self.Parameters['-max_percent_diff'],\ self.Parameters['-bp_window'],\ self.Parameters['-align_window'],\ self.Parameters['-single_bp_inserts']] command_part2.append(self._command_delimiter.join(filter(\ None,(map(str,lista))))) return self._command_delimiter.join(command_part1).strip(),\ self._command_delimiter.join(command_part2).strip() BaseCommand = property(_get_base_command)