annotate SMART/Java/Python/GetReadDistribution.py @ 6:769e306b7933

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1 #! /usr/bin/env python
2 #
3 # Copyright INRA-URGI 2009-2010
4 # 
5 # This software is governed by the CeCILL license under French law and
6 # abiding by the rules of distribution of free software. You can use,
7 # modify and/ or redistribute the software under the terms of the CeCILL
8 # license as circulated by CEA, CNRS and INRIA at the following URL
9 # "http://www.cecill.info".
10 # 
11 # As a counterpart to the access to the source code and rights to copy,
12 # modify and redistribute granted by the license, users are provided only
13 # with a limited warranty and the software's author, the holder of the
14 # economic rights, and the successive licensors have only limited
15 # liability.
16 # 
17 # In this respect, the user's attention is drawn to the risks associated
18 # with loading, using, modifying and/or developing or reproducing the
19 # software by the user in light of its specific status of free software,
20 # that may mean that it is complicated to manipulate, and that also
21 # therefore means that it is reserved for developers and experienced
22 # professionals having in-depth computer knowledge. Users are therefore
23 # encouraged to load and test the software's suitability as regards their
24 # requirements in conditions enabling the security of their systems and/or
25 # data to be ensured and, more generally, to use and operate it in the
26 # same conditions as regards security.
27 # 
28 # The fact that you are presently reading this means that you have had
29 # knowledge of the CeCILL license and that you accept its terms.
30 #
31 import random, os, glob, subprocess
32 from commons.core.parsing.ParserChooser import ParserChooser
33 from commons.core.parsing.GffParser import GffParser
34 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
35 from SMART.Java.Python.misc.Progress import Progress
36 from SMART.Java.Python.misc import Utils
37 from commons.core.LoggerFactory import LoggerFactory
38 from commons.core.utils.RepetOptionParser import RepetOptionParser
39 
40 LOG_DEPTH      = "smart"
41 DEFAULT_REGION = "_all_"
42 MULTIPLE_STR   = {1: "", 1000: " (in kpb)", 1000000: " (in Gbp)"}
43 
44 class GetReadDistribution(object):
45 
46 	def __init__(self, verbosity = 0):
47 		self.xLab         = ""
48 		self.yLab         = "# reads"
49 		self.verbosity    = verbosity
50 		self.number       = random.randint(0, 100000)
51 		self.log          = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self.verbosity)
52 		self.parsers      = {}
53 		self.distribution = {}
54 		self.factors      = {}
55 		self.regions      = None
56 		self.tmpDatName   = None
57 		self.tmpRName     = None
58 		self.quorum       = 1
59 		self.width        = 800
60 		self.height       = 300
61 
62 	def setNames(self, names):
63 		self.names = names
64 
65 	def setInputFiles(self, fileNames, format):
66 		chooser = ParserChooser(self.verbosity)
67 		chooser.findFormat(format)
68 		for cpt, fileName in enumerate(fileNames):
69 			self.parsers[self.names[cpt]] = chooser.getParser(fileName)
70 
71 	def setOutputFileName(self, fileName):
72 		self.outputFileName = fileName
73 
74 	def setLabs(self, xLab, yLab):
75 		self.xLab = xLab
76 		self.yLab = yLab
77 
78 	def setBinSize(self, binSize):
79 		self.binSize = binSize
80 
81 	def setColors(self, colors):
82 		self.colors = colors
83 
84 	def setFactors(self, factors):
85 		self.factors = dict(zip(self.names, factors))
86 
87 	def setMultiple(self, boolean):
88 		self.multiple = boolean
89 	
90 	def setImageSize(self, width, height):
91 		if width != None:
92 			self.width = width
93 		if height != None:
94 			self.height = height
95 
96 	def setQuorum(self, quorum):
97 		self.quorum = quorum
98 
99 	def setRegionsFile(self, fileName):
00 		if fileName != None:
01 			self._loadRegions(fileName)
02 
03 	def _checkOptions(self):
04 		if not self.parsers:
05 			self.logAndRaise("ERROR: Missing input file names")
06 
07 	def _logAndRaise(self, errorMsg):
08 		self.log.error(errorMsg)
09 		raise Exception(errorMsg)
10 
11 	def _loadRegions(self, fileName):
12 		self.regions = {}
13 		parser       = GffParser(fileName, self.verbosity)
14 		for transcript in parser.getIterator():
15 			chromosome = transcript.getChromosome()
16 			start      = transcript.getStart()
17 			end        = transcript.getEnd()
18 			name       = transcript.getName()
19 			if chromosome not in self.regions:
20 				self.regions[chromosome] = {}
21 			if start not in self.regions[chromosome]:
22 				self.regions[chromosome][start] = {}
23 			if end not in self.regions[chromosome][start]:
24 				self.regions[chromosome][start][end] = []
25 			self.regions[chromosome][start][end].append(name)
26 
27 	def _getRegions(self, transcript):
28 		if self.regions == None:
29 			return [DEFAULT_REGION]
30 		chromosome = transcript.getChromosome()
31 		start      = transcript.getStart()
32 		end        = transcript.getEnd()
33 		if chromosome not in self.regions:
34 			return []
35 		names = []
36 		for loadedStart in sorted(self.regions[chromosome].keys()):
37 			if loadedStart > end:
38 				return names
39 			for loadedEnd in reversed(sorted(self.regions[chromosome][loadedStart].keys())):
40 				if loadedEnd < start:
41 					break
42 				names.extend(self.regions[chromosome][loadedStart][loadedEnd])
43 		return names
44 
45 	def _parse(self, name):
46 		progress = UnlimitedProgress(10000, "Reading file '%s'" % (name), self.verbosity)
47 		for transcript in self.parsers[name].getIterator():
48 			if transcript.__class__.__name__ == "Mapping":
49 				transcript = transcript.getTranscript()
50 			regions = self._getRegions(transcript)
51 			for region in regions:
52 				if region not in self.distribution:
53 					self.distribution[region] = {}
54 				if name not in self.distribution[region]:
55 					self.distribution[region][name] = {}
56 				chromosome  = transcript.getChromosome()
57 				nbElements  = float(transcript.getTagValue("nbElements")) if "nbElements" in transcript.getTagNames() else 1
58 				nbElements *= self.factors.get(name, 1)
59 				if chromosome not in self.distribution[region][name]:
60 					self.distribution[region][name][chromosome] = {}
61 				previousBin = None
62 				for exon in transcript.getExons():
63 					for pos in range(exon.getStart(), exon.getEnd()+1):
64 						bin = pos / self.binSize
65 						if bin != previousBin:
66 							self.distribution[region][name][chromosome][bin] = self.distribution[region][name][chromosome].get(bin, 0) + nbElements
67 							previousBin = bin
68 			progress.inc()
69 		progress.done()
70 
71 	def _checkQuorum(self, region):
72 		if self.quorum == None:
73 			return True
74 		return max([max([max(self.distribution[region][name][chromosome].values()) for chromosome in self.distribution[region][name]]) for name in self.distribution[region]]) >= self.quorum
75 
76 	def _writeData(self, region):
77 		self.tmpDatName = "tmpFile%d.dat" % (self.number)
78 		handle          = open(self.tmpDatName, "w")
79 		handle.write("Chr\tPos\tCount\tSample\n")
80 		for name in self.distribution[region]:
81 			for chromosome in sorted(self.distribution[region][name].keys()):
82 				for pos in sorted(self.distribution[region][name][chromosome].keys()):
83 					handle.write("%s\t%d\t%d\t\"%s\"\n" % (chromosome, pos * self.binSize, self.distribution[region][name][chromosome].get(pos, 0), name))
84 		handle.close()
85 
86 	def _findMultiple(self, region):
87 		if not self.multiple:
88 			return 1
89 		maxPosition = max([self.distribution[region][name][chromosome].keys() for name in self.distribution[region] for chromosome in self.distribution[region][name]])
90 		if maxPosition > 2000000:
91 			return 1000000
92 		elif maxPosition > 2000:
93 			return 1000
94 		return 1
95 
96 	def _writeScript(self, region):
97 		self.tmpRName = "tmpFile%d.R" % (self.number)
98 		fileName      = self.outputFileName if region == DEFAULT_REGION else "%s_%s.png" % (os.path.splitext(self.outputFileName)[0], region)
99 		colors        = "scale_fill_brewer(palette=\"Set1\") + scale_color_brewer(palette=\"Set1\")" if self.colors == None else "scale_fill_manual(values = c(%s)) + scale_color_manual(values = c(%s))" % (", ".join(["\"%s\"" % (color) for color in self.colors]), ", ".join(["\"%s\"" % (color) for color in self.colors]))
00 		title         = "" if region == DEFAULT_REGION else " of %s" % (region)
01 		facet         = "Sample ~ Chr" if region == DEFAULT_REGION else "Sample ~ ."
02 		handle        = open(self.tmpRName, "w")
03 		multiple      = self._findMultiple(region)
04 		handle.write("library(ggplot2)\n")
05 		handle.write("data <- read.table(\"%s\", header = T)\n" % (self.tmpDatName))
06 		handle.write("data$Sample <- factor(data$Sample, levels=c(%s))\n" % (", ".join(["\"%s\"" % (name) for name in self.names])))
07 		handle.write("png(\"%s\", width = %d, height = %d)\n" % (fileName, self.width, self.height))
08 		handle.write("ggplot(data, aes(x = Pos/%d, y = Count, fill = Sample, color = Sample)) + opts(title = \"Distribution%s\") + geom_bar(stat = \"identity\") + facet_grid(%s, space=\"free\") + xlab(\"%s%s\") + ylab(\"%s\") + %s + opts(legend.position = \"none\", panel.grid.major = theme_blank(), panel.grid.minor = theme_blank(), panel.background = theme_blank())\n" % (multiple, title, facet, self.xLab, MULTIPLE_STR[multiple], self.yLab, colors))
09 		handle.write("dev.off()\n")
10 
11 	def _runR(self):
12 		rCommand = "R"
13 		if "SMARTRPATH" in os.environ:
14 			rCommand = os.environ["SMARTRPATH"]
15 		command = "\"%s\" CMD BATCH %s" % (rCommand, self.tmpRName)
16 		status = subprocess.call(command, shell=True)
17 		if status != 0:
18 			raise Exception("Problem with the execution of script file %s, status is: %s" % (self.tmpRName, status))
19 
20 	def _plot(self):
21 		progress = Progress(len(self.distribution), "Plotting data", self.verbosity)
22 		for region in self.distribution:
23 			if not self._checkQuorum(region):
24 				self.log.info("Not displaying '%s' for it contains insufficient data." % (region))
25 			else:
26 				self._writeData(region)
27 				self._writeScript(region)
28 				self._runR()
29 			progress.inc()
30 		progress.done()
31 
32 	def _cleanFiles(self):
33 		for fileName in (self.tmpDatName, self.tmpRName):
34 			if fileName != None and os.path.exists(fileName):
35 				os.remove(fileName)
36 				for otherFileName in glob.glob("%s*" % (fileName)):
37 					os.remove(otherFileName)
38 
39 	def run(self):
40 		LoggerFactory.setLevel(self.log, self.verbosity)
41 		self._checkOptions()
42 		self.log.info("START Get Read Distribution")
43 		for name in self.names:
44 			self._parse(name)
45 		self._plot()
46 		self._cleanFiles()
47 		self.log.info("END Get Read Distribution")
48 
49 
50 if __name__ == "__main__":
51 	description = "Usage: GetReadDistribution.py [options]\n\nGet Read Distribution v1.0.1: Get the distribution of a set of reads. [Category: Personal]\n"
52 	epilog = ""
53 	parser = RepetOptionParser(description = description, epilog = epilog)
54 	parser.add_option("-i", "--input",     dest="inputFileNames",  action="store",      default=None,      type="string", help="input files, separated by commas [compulsory] [format: string]")
55 	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]")
56 	parser.add_option("-n", "--names",     dest="names",           action="store",      default=None,      type="string", help="name of the input data, separated by commas [compulsory] [format: string]")
57 	parser.add_option("-o", "--output",    dest="outputFileName",  action="store",      default=None,      type="string", help="output file [format: output file in PNG format]")
58 	parser.add_option("-s", "--binSize",   dest="binSize",         action="store",      default=10000,     type="int",    help="bin size [format: int] [default: 10000]")
59 	parser.add_option("-l", "--xLabel",    dest="xLab",            action="store",      default="",        type="string", help="x-axis label name [format: string]")
60 	parser.add_option("-L", "--yLabel",    dest="yLab",            action="store",      default="# reads", type="string", help="y-axis label name [format: string] [default: Reads]")
61 	parser.add_option("-c", "--colors",    dest="colors",          action="store",      default=None,      type="string", help="colors of the bars, separated by commas  [format: string]")
62 	parser.add_option("-a", "--factors",   dest="factors",         action="store",      default=None,      type="string", help="normalization factors, separated by commas  [format: string]")
63 	parser.add_option("-r", "--regions",   dest="regionsFileName", action="store",      default=None,      type="string", help="regions to plot [format: transcript file in GFF format]")
64 	parser.add_option("-m", "--multiple",  dest="multiple",        action="store_true", default=False,                    help="print position using multiples (k, G) [format: boolean] [default: False]")
65 	parser.add_option("-q", "--quorum",    dest="quorum",          action="store",      default=1,         type="int",    help="minimum number of intervals to plot a region [format: int] [default: 1]")
66 	parser.add_option("-z", "--width",     dest="width",           action="store",      default=800,       type="int",    help="width of the image [format: int] [default: 800]")
67 	parser.add_option("-Z", "--height",    dest="height",          action="store",      default=300,       type="int",    help="height of the image [format: int] [default: 300]")
68 	parser.add_option("-v", "--verbosity", dest="verbosity",       action="store",      default=1,         type="int",    help="trace level [format: int]")
69 	options = parser.parse_args()[0]
70 	iGetReadDistribution = GetReadDistribution(options.verbosity)
71 	iGetReadDistribution.setNames(options.names.split(","))
72 	iGetReadDistribution.setInputFiles(options.inputFileNames.split(","), options.format)
73 	iGetReadDistribution.setOutputFileName(options.outputFileName)
74 	iGetReadDistribution.setLabs(options.xLab, options.yLab)
75 	iGetReadDistribution.setBinSize(options.binSize)
76 	iGetReadDistribution.setColors(None if options.colors == None else options.colors.split(","))
77 	iGetReadDistribution.setFactors(None if options.factors == None else map(float, options.factors.split(",")))
78 	iGetReadDistribution.setRegionsFile(options.regionsFileName)
79 	iGetReadDistribution.setMultiple(options.multiple)
80 	iGetReadDistribution.setQuorum(options.quorum)
81 	iGetReadDistribution.setImageSize(options.width, options.height)
82 	iGetReadDistribution.run()
83