view smart_toolShed/SMART/Java/Python/ncList/NCIndex.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

#! /usr/bin/env python
#
# Copyright INRA-URGI 2009-2010
# 
# This software is governed by the CeCILL license under French law and
# abiding by the rules of distribution of free software. You can use,
# modify and/ or redistribute the software under the terms of the CeCILL
# license as circulated by CEA, CNRS and INRIA at the following URL
# "http://www.cecill.info".
# 
# As a counterpart to the access to the source code and rights to copy,
# modify and redistribute granted by the license, users are provided only
# with a limited warranty and the software's author, the holder of the
# economic rights, and the successive licensors have only limited
# liability.
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# In this respect, the user's attention is drawn to the risks associated
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# software by the user in light of its specific status of free software,
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# The fact that you are presently reading this means that you have had
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from SMART.Java.Python.structure.Transcript import Transcript

class NCIndex(object):

    def __init__(self, verbosity):
        self._verbosity = verbosity
        self._step      = 10000
        self._indices   = []

    def setStep(self, step):
        self._step = step

    def addTranscript(self, end, index):
        binStart = len(self._indices)
        binEnd   = int(end / self._step)
        for bin in range(binStart, binEnd+1):
            self._indices.append(index)

    def getIndex(self, transcript):
        bin = int(transcript.getStart() / self._step)
        if bin >= len(self._indices):
            return self._indices[-1]
        return self._indices[bin]