| Previous changeset 7:86c781421239 (2013-01-18) Next changeset 9:1eb55963fe39 (2013-03-14) |
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Commit message:
Deleted selected files |
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removed:
SMART/Java/Python/toolLauncher/RnaFoldLauncher.py SMART/Java/Python/toolLauncher/__init__.py |
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| diff -r 86c781421239 -r 4dded8b1fbc4 SMART/Java/Python/toolLauncher/RnaFoldLauncher.py --- a/SMART/Java/Python/toolLauncher/RnaFoldLauncher.py Fri Jan 18 09:01:23 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,379 +0,0 @@\n-#\n-# Copyright INRA-URGI 2009-2010\n-# \n-# This software is governed by the CeCILL license under French law and\n-# abiding by the rules of distribution of free software. You can use,\n-# modify and/ or redistribute the software under the terms of the CeCILL\n-# license as circulated by CEA, CNRS and INRIA at the following URL\n-# "http://www.cecill.info".\n-# \n-# As a counterpart to the access to the source code and rights to copy,\n-# modify and redistribute granted by the license, users are provided only\n-# with a limited warranty and the software\'s author, the holder of the\n-# economic rights, and the successive licensors have only limited\n-# liability.\n-# \n-# In this respect, the user\'s attention is drawn to the risks associated\n-# with loading, using, modifying and/or developing or reproducing the\n-# software by the user in light of its specific status of free software,\n-# that may mean that it is complicated to manipulate, and that also\n-# therefore means that it is reserved for developers and experienced\n-# professionals having in-depth computer knowledge. Users are therefore\n-# encouraged to load and test the software\'s suitability as regards their\n-# requirements in conditions enabling the security of their systems and/or\n-# data to be ensured and, more generally, to use and operate it in the\n-# same conditions as regards security.\n-# \n-# The fact that you are presently reading this means that you have had\n-# knowledge of the CeCILL license and that you accept its terms.\n-#\n-import os\n-import sys\n-import random\n-import subprocess\n-from SMART.Java.Python.structure.TranscriptList import TranscriptList\n-from SMART.Java.Python.structure.Transcript import Transcript\n-from SMART.Java.Python.misc.Progress import Progress\n-from commons.core.parsing.FastaParser import FastaParser\n-\n-\n-class RnaFoldStructure(object):\n- """\n- A structure to store the output of RNAFold\n- @ivar name: the name of the sequence\n- @type name: string\n- @ivar sequence: the sequence (with gaps)\n- @type sequence: string\n- @ivar structure: the bracket structure\n- @type structure: string\n- @ivar energy: the energy of the fold\n- @type energy: float\n- @ivar interactions: the interactions inside the structure\n- @ivar interactions: the interactions inside the structure\n- """\n-\n- def __init__(self, name, sequence, structure, energy):\n- """\n- Initialize the structure\n- @param name the name of the sequence\n- @type name: string\n- @param sequence: the sequence (with gaps)\n- @type sequence: string\n- @param structure: the bracket structure\n- @type structure: string\n- @param energy: the energy of the fold\n- @type energy: float\n- """\n- self.name = name \n- self.sequence = sequence\n- self.structure = structure\n- self.energy = energy\n- self.interactions = None\n-\n- \n- def analyze(self):\n- """\n- Analyze the output, assign the interactions\n- """\n- if len(self.sequence) != len(self.structure):\n- sys.exit("Sizes of sequence and structure differ (\'%s\' and \'%s\')!\\n" % (self.sequence, self.structure))\n- stack = []\n- self.interactions = [None for i in range(len(self.sequence))]\n- for i in range(len(self.sequence)):\n- if self.structure[i] == "(":\n- stack.append(i)\n- elif self.structure[i] == ")":\n- if not stack:\n- sys.exit("Something wrong in the interaction line \'%s\'!\\n" % (self.structure))\n- otherI = stack.pop()\n- self.interactions[i] = otherI\n- self.interactions[otherI] = i\n- if stack:\n- sys.exit("Something wrong in the interaction line \'%s\'!\\n" % (self.structure))\n-\n-\n- def getNbBulges(self, sta'..b'\n- @type rnaFoldOutput: class L{RnaFoldStructure<RnaFoldStructure>}\n- @ivar reverse: invert the extensions\n- @type reverse: bool\n- @return: a t-uple of energy, number of insertions, number of bulges, strand\n- """\n- rnaFoldOutput.analyze()\n- transcriptSize = transcript.end - transcript.start + 1\n- start = fivePrimeExtension if not reverse else threePrimeExtension\n- end = start + transcriptSize\n- energy = rnaFoldOutput.energy\n- nbBulges = rnaFoldOutput.getNbBulges(start, end)\n- (minStar, maxStar) = rnaFoldOutput.getStar(start, end)\n- minStar += transcript.start - start\n- maxStar += transcript.start - start\n- if self.verbosity > 100:\n- print "Getting structure with energy %d, nbBulges %d, miRna* %d-%d, strand %s" % (energy, nbBulges, minStar, maxStar, "-" if reverse else "+")\n- return (energy, nbBulges, minStar, maxStar, reverse)\n-\n- \n- def fold(self, transcript):\n- """\n- Fold a transcript (in each strand)\n- @ivar transcript: a transcript\n- @type transcript: class L{Transcript<Transcript>}\n- @return: a t-uple of energy, number of insertions, number of bulges, strand\n- """\n- results = [None] * self.nbStrands\n- strands = [False, True] if self.nbStrands == 2 else [False]\n- minNbBulges = 1000000\n- for i, reverse in enumerate(strands):\n- self.writeInputFile(transcript, reverse, self.fivePrimeExtension, self.threePrimeExtension)\n- self.startRnaFold()\n- output = self.parseRnaFoldOutput()\n- results[i] = self.analyzeRnaFoldOutput(transcript, output, reverse, self.fivePrimeExtension, self.threePrimeExtension)\n- minNbBulges = min(minNbBulges, results[i][1])\n- for result in results:\n- if result[1] == minNbBulges:\n- return result\n- return None\n-\n-\n- def refold(self, transcript):\n- """\n- Fold a transcript, knowing where the miRNA starts and end\n- @ivar transcript: a transcript\n- @type transcript: class L{Transcript<Transcript>}\n- @return: the energy\n- """\n- miStar = transcript.getTagValue("miRnaStar")\n- startMiStar = int(miStar.split("-")[0])\n- endMiStart = int(miStar.split("-")[1])\n- fivePrimeExtension = max(0, transcript.start - startMiStar) + 5\n- threePrimeExtension = max(0, endMiStart - transcript.end) + 5\n- self.writeInputFile(transcript, False, fivePrimeExtension, threePrimeExtension)\n- self.startRnaFold()\n- output = self.parseRnaFoldOutput()\n- result = self.analyzeRnaFoldOutput(transcript, output, False, fivePrimeExtension, threePrimeExtension)\n- return result[0]\n-\n-\n- def computeResults(self):\n- """\n- Fold all and fill an output transcript list with the values\n- """\n- progress = Progress(self.inputTranscriptList.getNbTranscripts(), "Handling transcripts", self.verbosity)\n- self.outputTranscriptList = TranscriptList()\n- for transcript in self.inputTranscriptList.getIterator():\n- result = self.fold(transcript)\n- transcript.setTagValue("nbBulges", result[1])\n- transcript.setTagValue("miRnaStar", "%d-%d" % (result[2], result[3]))\n- transcript.setTagValue("miRNAstrand", result[4])\n- transcript.setTagValue("energy", self.refold(transcript))\n- self.outputTranscriptList.addTranscript(transcript)\n- progress.inc()\n- progress.done()\n-\n-\n- def getResults(self):\n- """\n- Get an output transcript list with the values\n- """\n- if self.outputTranscriptList == None:\n- self.computeResults()\n- return self.outputTranscriptList\n' |