view smart_toolShed/SMART/Java/Python/cleanGff.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
# with loading, using, modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
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# encouraged to load and test the software's suitability as regards their
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"""
Clean a GFF file (as given by NCBI or TAIR) and outputs a GFF3 file.
"""

import os
import re
from optparse import OptionParser
from commons.core.parsing.GffParser import *
from SMART.Java.Python.misc.RPlotter import *
from SMART.Java.Python.misc.Progress import Progress
from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress

count = {}

class ParsedLine(object):
    def __init__(self, line, cpt):
        self.line = line
        self.cpt  = cpt
        self.parse()

    def parse(self):
        self.line = self.line.strip()
        self.splittedLine = self.line.split(None, 8)
        if len(self.splittedLine) < 9:
            raise Exception("Line '%s' has less than 9 fields.  Exiting..." % (self.line))
        self.type = self.splittedLine[2]
        self.parseOptions()
        self.getId()
        self.getParents()

    def parseOptions(self):
        self.parsedOptions = {}
        for option in self.splittedLine[8].split(";"):
            option = option.strip()
            if option == "": continue
            posSpace = option.find(" ")
            posEqual = option.find("=")
            if posEqual != -1 and (posEqual < posSpace or posSpace == -1):
                key, value = option.split("=", 1)
            elif posSpace != -1:
                key, value = option.split(None, 1)
            else:
                key   = "ID"
                value = option
            self.parsedOptions[key.strip()] = value.strip(" \"")

    def getId(self):
        for key in self.parsedOptions:
            if key.lower() == "id":
                self.id = self.parsedOptions[key]
                return
        if "Parent" in self.parsedOptions:
            parent = self.parsedOptions["Parent"].split(",")[0]
            if parent not in count:
                count[parent] = {}
            if self.type not in count[parent]:
                count[parent][self.type] = 0
            count[parent][self.type] += 1
            self.id = "%s-%s-%d" % (parent, self.type, count[parent][self.type])
        else:
            self.id = "smart%d" % (self.cpt)
        self.parsedOptions["ID"] = self.id

    def getParents(self):
        for key in self.parsedOptions:
            if key.lower() in ("parent", "derives_from"):
                self.parents = self.parsedOptions[key].split(",")
                return
        self.parents = None

    def removeParent(self):
        for key in self.parsedOptions.keys():
            if key.lower() in ("parent", "derives_from"):
                del self.parsedOptions[key]

    def export(self):
        self.splittedLine[8] = ";".join(["%s=%s" % (key, value) for key, value in self.parsedOptions.iteritems()])
        return "%s\n" % ("\t".join(self.splittedLine))


class CleanGff(object):

    def __init__(self, verbosity = 1):
        self.verbosity = verbosity
        self.lines         = {}
        self.acceptedTypes = []
        self.parents       = []
        self.children      = {}

    def setInputFileName(self, name):
        self.inputFile = open(name)
        
    def setOutputFileName(self, name):
        self.outputFile = open(name, "w")

    def setAcceptedTypes(self, types):
        self.acceptedTypes = types

    def parse(self):
        progress = UnlimitedProgress(100000, "Reading input file", self.verbosity)
        for cpt, line in enumerate(self.inputFile):
            if not line or line[0] == "#": continue
            if line[0] == ">": break
            parsedLine = ParsedLine(line, cpt)
            if parsedLine.type in self.acceptedTypes:
                self.lines[parsedLine.id] = parsedLine
            progress.inc()
        progress.done()

    def sort(self):
        progress = Progress(len(self.lines.keys()), "Sorting file", self.verbosity)
        for line in self.lines.values():
            parentFound = False
            if line.parents:
                for parent in line.parents:
                    if parent in self.lines:
                        parentFound = True
                        if parent in self.children:
                            self.children[parent].append(line)
                        else:
                            self.children[parent] = [line]
            if not parentFound:
                line.removeParent()
                self.parents.append(line)
            progress.inc()
        progress.done()

    def write(self):
        progress = Progress(len(self.parents), "Writing output file", self.verbosity)
        for line in self.parents:
            self.writeLine(line)
            progress.inc()
        self.outputFile.close()
        progress.done()

    def writeLine(self, line):
        self.outputFile.write(line.export())
        if line.id in self.children:
            for child in self.children[line.id]:
                self.writeLine(child)

    def run(self):
        self.parse()
        self.sort()
        self.write()


if __name__ == "__main__":
    
    # parse command line
    description = "Clean GFF v1.0.3: Clean a GFF file (as given by NCBI) and outputs a GFF3 file. [Category: Other]"

    parser = OptionParser(description = description)
    parser.add_option("-i", "--input",     dest="inputFileName",  action="store",                      type="string", help="input file name [compulsory] [format: file in GFF format]")
    parser.add_option("-o", "--output",    dest="outputFileName", action="store",                      type="string", help="output file [compulsory] [format: output file in GFF3 format]")
    parser.add_option("-t", "--types",     dest="types",          action="store", default="mRNA,exon", type="string", help="list of comma-separated types that you want to keep [format: string] [default: mRNA,exon]")
    parser.add_option("-v", "--verbosity", dest="verbosity",      action="store", default=1,           type="int",    help="trace level [format: int]")
    (options, args) = parser.parse_args()

    cleanGff = CleanGff(options.verbosity)
    cleanGff.setInputFileName(options.inputFileName)
    cleanGff.setOutputFileName(options.outputFileName)
    cleanGff.setAcceptedTypes(options.types.split(","))
    cleanGff.run()