/usr/lib/python2.7/dist-packages/cogent/app/rnaalifold.py is in python-cogent 1.9-9.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 | #!/usr/bin/env python
from cogent.app.util import CommandLineApplication,\
CommandLineAppResult, ResultPath
from cogent.app.parameters import Parameter, FlagParameter, ValuedParameter,\
MixedParameter,Parameters, _find_synonym
from cogent.core.alignment import Alignment
from cogent.core.moltype import RNA
from cogent.parse.fasta import MinimalFastaParser
from cogent.parse.rnaalifold import rnaalifold_parser, MinimalRnaalifoldParser
from cogent.format.clustal import clustal_from_alignment
from cogent.struct.rna2d import ViennaStructure
__author__ = "Shandy Wikman"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__contributors__ = ["Shandy Wikman","Jeremy Widmann"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Shandy Wikman"
__email__ = "ens01svn@cs.umu.se"
__status__ = "Development"
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
def rnaalifold_from_alignment(aln,moltype=RNA,params=None):
"""Returns seq, pairs, folding energy for alignment.
"""
#Create Alignment object. Object will handle if seqs are unaligned.
aln = Alignment(aln,MolType=RNA)
int_map, int_keys = aln.getIntMap()
app = RNAalifold(WorkingDir='/tmp',\
InputHandler='_input_as_multiline_string',params=params)
res = app(clustal_from_alignment(int_map))
#seq,pairs,energy = rnaalifold_parser(res['StdOut'].readlines())
pairs_list = MinimalRnaalifoldParser(res['StdOut'].readlines())
res.cleanUp()
return pairs_list
if __name__ == "__main__":
from sys import argv
aln_file = argv[1]
aln = dict(MinimalFastaParser(open(aln_file,'U')))
res = rnaalifold_from_alignment(aln)
print res
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