annotate smart_toolShed/SMART/Java/Python/getSizes.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".
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# 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
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import os, sys
from optparse import OptionParser
from commons.core.parsing.FastaParser import FastaParser
from commons.core.parsing.FastqParser import FastqParser
from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
from commons.core.parsing.GffParser import GffParser
from SMART.Java.Python.misc.Progress import Progress
from SMART.Java.Python.misc.RPlotter import RPlotter
from SMART.Java.Python.misc import Utils

from commons.core.LoggerFactory import LoggerFactory
from commons.core.utils.RepetOptionParser import RepetOptionParser

LOG_DEPTH = "smart"

class GetSizes(object):
    
    def __init__(self, inFileName = None, inFormat=None, outFileName = None, query=None,xMax=None, xMin=None, csv=False, verbosity = 0):
        self.inFileName = inFileName
        self.inFormat= inFormat
        self.outFileName = outFileName
        self.query = query
        self.xMax = xMax
        self.xMin = xMin
        self.xLab = "Size"
        self.yLab = "# reads"
        self.barplot = False
        self.csv = csv
        self._verbosity = verbosity
        self.parser = None
        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
        
    def setAttributesFromCmdLine(self):
        description = "Usage: getSizes.py [options]\n\nGet Sizes v1.0.2: Get the sizes of a set of genomic coordinates. [Category: Visualization]\n"
        epilog = ""
        parser = RepetOptionParser(description = description, epilog = epilog)
        parser.add_option("-i", "--input",     dest="inputFileName",  action="store",      default=None,      type="string", help="input file [compulsory] [format: file in transcript or sequence format given by -f]")
        parser.add_option("-f", "--format",    dest="format",         action="store",      default=None,      type="string", help="format of the input [compulsory] [format: transcript or sequence file format]")
        parser.add_option("-q", "--query",     dest="query",          action="store",      default=None,      type="string", help="type to mesure [default: size] [format: choice (size, intron size, exon size, 1st exon size)]")     
        parser.add_option("-o", "--output",    dest="outputFileName", action="store",      default=None,      type="string", help="output file [format: output file in PNG format]")
        parser.add_option("-x", "--xMax",      dest="xMax",           action="store",      default=None,      type="int",    help="maximum value on the x-axis to plot [format: int]")
        parser.add_option("-X", "--xMin",      dest="xMin",           action="store",      default=None,      type="int",    help="minimum value on the x-axis to plot [format: int]")
        parser.add_option("-v", "--verbosity", dest="verbosity",      action="store",      default=1,         type="int",    help="trace level [format: int]")
        parser.add_option("-c", "--csv",       dest="csv",            action="store",                         type="string", help="write a .csv file [format: bool] [default: false]")
        parser.add_option("-a", "--xLabel",    dest="xLab",           action="store",      default="Size",    type="string", help="x absis label name [format: string] [default: Size]")
        parser.add_option("-b", "--yLabel",    dest="yLab",           action="store",      default="# reads", type="string", help="y absis label name [format: string] [default: Reads]")
        parser.add_option("-B", "--barplot",   dest="barplot",        action="store_true", default=False,                    help="use barplot representation [format: bool] [default: false]")  
        options = parser.parse_args()[0]
        self._setAttributesFromOptions(options)
        
    def _setAttributesFromOptions(self, options):
        self.setInFileName(options.inputFileName)
        self.setInFormat(options.format)
        self.setQuery(options.query)
        self.setOutFileName(options.outputFileName)
        self.setXMax(options.xMax)
        self.setXMin(options.xMin)
        self.setxLab(options.xLab)
        self.setyLab(options.yLab)
        self.setBarplot(options.barplot)
        self.setVerbosity(options.verbosity)
        
    def setInFileName(self, inputFileName):
        self.inFileName = inputFileName
        
    def setInFormat(self, inFormat):
        self.inFormat = inFormat
    
    def setQuery(self, query):
        self.query = query
        
    def setOutFileName(self, outFileName):
        self.outFileName = outFileName
    
    def setXMax(self, xMax):
        self.xMax = xMax
        
    def setXMin(self, xMin):
        self.xMin = xMin
    
    def setxLab(self, xLab):
        self.xLab = xLab
        
    def setyLab(self, yLab):
        self.yLab = yLab
        
    def setBarplot(self, barplot):
        self.barplot = barplot
        
    def setCsv(self, csv):
        self.csv = csv
        
    def setVerbosity(self, verbosity):
        self._verbosity = verbosity
        
    def _checkOptions(self):
        if self.inFileName == None:
            self._logAndRaise("ERROR: Missing input file name")
        if self.inFormat == "fasta":
            self.parser = FastaParser(self.inFileName, self._verbosity)
        elif self.inFormat == "fastq":
            self.parser = FastqParser(self.inFileName, self._verbosity)
        else:
            self.parser = TranscriptContainer(self.inFileName, self.inFormat, self._verbosity)
            
    def _logAndRaise(self, errorMsg):
        self._log.error(errorMsg)
        raise Exception(errorMsg)
                    
    def run(self):
        LoggerFactory.setLevel(self._log, self._verbosity)
        self._checkOptions()
        self._log.info("START getsizes")
        self._log.debug("Input file name: %s" % self.inFileName)

        nbItems = self.parser.getNbItems()
        self._log.info( "%i items found" % (nbItems))
        
        # treat items
        progress   = Progress(nbItems, "Analyzing sequences of %s" % (self.inFileName), self._verbosity)
        sizes      = {}
        names      = {}
        minimum    = 1000000000000
        maximum    = 0
        sum        = 0
        number     = 0
        nbSubItems = 0
        for item in self.parser.getIterator():
            items = []
            if self.query == "exon":
                items = item.getExons()
            elif self.query == "exon1":
                if len(item.getExons()) > 1:
                    item.sortExons()
                    items = [item.getExons()[0]]
            elif self.query == "intron":
                items = item.getIntrons()
            else:
                items = [item, ]
    
            for thisItem in items:
                try:
                    nbElements = int(float(thisItem.getTagValue("nbElements")))
                    if nbElements == None:
                        nbElements = 1
                except:
                    nbElements = 1
                size    = thisItem.getSize()
                minimum = min(minimum, size)
                maximum = max(maximum, size)
                name    = thisItem.name.split()[0]
                
                if size not in sizes:
                    sizes[size] = nbElements
                    if self.csv:
                        names[size] = [name, ]
                else:
                    sizes[size] += nbElements
                    if self.csv:
                        names[size].append(name)
                sum        += size
                nbSubItems += nbElements
            number += 1
            progress.inc()
        progress.done()

        if self.outFileName != None:
            plotter = RPlotter(self.outFileName, self._verbosity)
            plotter.setFill(0)
            plotter.setMinimumX(self.xMin)
            plotter.setMaximumX(self.xMax)
            plotter.setXLabel(self.xLab)
            plotter.setYLabel(self.yLab)
            plotter.setBarplot(self.barplot)
            plotter.addLine(sizes)
            plotter.plot()
            
        if nbSubItems == 0:
            self._logAndRaise("No item found")
            
        if self.csv:
            csvHandle = open(self.csv, "w")
            for size in range(min(sizes.keys()), max(sizes.keys())+1):
                if size not in sizes:
                    csvHandle.write("%d,0,\n" % (size))
                else:
                    csvHandle.write("%d,%d,%s\n" % (size, sizes[size], ";".join(names[size])))
            csvHandle.close()
        
        self.items = number      
        self.subItems = nbSubItems
        self.nucleotides = sum
        self.minAvgMedMax = Utils.getMinAvgMedMax(sizes)
                  
        print "%d items" % (number)
        print "%d sub-items" % (nbSubItems)
        print "%d nucleotides" % (sum)
        print "min/avg/med/max transcripts: %d/%.2f/%.1f/%d" % Utils.getMinAvgMedMax(sizes)

        self._log.info("END getsizes")


if __name__ == "__main__":
    iGetSizes = GetSizes()
    iGetSizes.setAttributesFromCmdLine()
    iGetSizes.run()
    
#TODO: add two more options!!!!!!