<reponame>861934367/cgat
##########################################################################
#
#   MRC FGU Computational Genomics Group
#
#   $Id: bed2graph.py 2861 2010-02-23 17:36:32Z andreas $
#
#   Copyright (C) 2009 <NAME>
#
#   This program is free software; you can redistribute it and/or
#   modify it under the terms of the GNU General Public License
#   as published by the Free Software Foundation; either version 2
#   of the License, or (at your option) any later version.
#
#   This program is distributed in the hope that it will be useful,
#   but WITHOUT ANY WARRANTY; without even the implied warranty of
#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#   GNU General Public License for more details.
#
#   You should have received a copy of the GNU General Public License
#   along with this program; if not, write to the Free Software
#   Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
##########################################################################
"""
bed2graph.py - compute the overlap graph between two bed files
==============================================================

:Author: <NAME>
:Release: $Id: bed2graph.py 2861 2010-02-23 17:36:32Z andreas $
:Date: |today|
:Tags: Python

Purpose
-------

This script ouputs a list of the names of all overlapping intervals 
between two bed files.

Usage
-----

Type::

   python bed2graph.py A.bed.gz B.bed.gz > graph.out

for command line help.

Command line options
--------------------

"""

import sys
import CGAT.Experiment as E
import CGAT.IOTools as IOTools
import CGAT.Bed as Bed


def main(argv=None):
    """script main.

    parses command line options in sys.argv, unless *argv* is given.
    """

    if not argv:
        argv = sys.argv

    # setup command line parser
    parser = E.OptionParser(
        version="%prog version: $Id: bed2graph.py 2861 2010-02-23 17:36:32Z andreas $", usage=globals()["__doc__"])

    parser.add_option("-o", "--output-section", dest="output", type="choice",
                      choices=("full", "name"),
                      help="output either ``full`` overlapping entries, only the ``name``s. [default=%default].")

    parser.set_defaults(
        output="full",
    )

    # add common options (-h/--help, ...) and parse command line
    (options, args) = E.Start(parser, argv=argv)

    if len(args) != 2:
        raise ValueError("two arguments required")

    if args[0] == "-":
        infile1 = options.stdin
    else:
        infile1 = IOTools.openFile(args[0], "r")

    infile2 = IOTools.openFile(args[1], "r")

    idx = Bed.readAndIndex(infile2, with_values=True)

    output = options.output
    outfile = options.stdout

    if output == "name":
        outfile.write("name1\tname2\n")
        outf = lambda x: x.fields[0]
    else:
        outf = str

    for bed in Bed.iterator(infile1):
        try:
            overlaps = idx[bed.contig].find(bed.start, bed.end)
        except (KeyError, IndexError):
            # ignore missing contig and zero length intervals
            continue

        for o in overlaps:
            outfile.write("\t".join((outf(bed), outf(o[2]))) + "\n")

    E.Stop()


if __name__ == "__main__":
    sys.exit(main(sys.argv))

##########################################################################
#
#   MRC FGU Computational Genomics Group
#
#   $Id: bed2graph.py 2861 2010-02-23 17:36:32Z andreas $
#
#   Copyright (C) 2009 <NAME>
#
#   This program is free software; you can redistribute it and/or
#   modify it under the terms of the GNU General Public License
#   as published by the Free Software Foundation; either version 2
#   of the License, or (at your option) any later version.
#
#   This program is distributed in the hope that it will be useful,
#   but WITHOUT ANY WARRANTY; without even the implied warranty of
#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#   GNU General Public License for more details.
#
#   You should have received a copy of the GNU General Public License
#   along with this program; if not, write to the Free Software
#   Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
##########################################################################
"""
bed2graph.py - compute the overlap graph between two bed files
==============================================================

:Author: <NAME>
:Release: $Id: bed2graph.py 2861 2010-02-23 17:36:32Z andreas $
:Date: |today|
:Tags: Python

Purpose
-------

This script ouputs a list of the names of all overlapping intervals 
between two bed files.

Usage
-----

Type::

   python bed2graph.py A.bed.gz B.bed.gz > graph.out

for command line help.

Command line options
--------------------

"""

import sys
import CGAT.Experiment as E
import CGAT.IOTools as IOTools
import CGAT.Bed as Bed


def main(argv=None):
    """script main.

    parses command line options in sys.argv, unless *argv* is given.
    """

    if not argv:
        argv = sys.argv

    # setup command line parser
    parser = E.OptionParser(
        version="%prog version: $Id: bed2graph.py 2861 2010-02-23 17:36:32Z andreas $", usage=globals()["__doc__"])

    parser.add_option("-o", "--output-section", dest="output", type="choice",
                      choices=("full", "name"),
                      help="output either ``full`` overlapping entries, only the ``name``s. [default=%default].")

    parser.set_defaults(
        output="full",
    )

    # add common options (-h/--help, ...) and parse command line
    (options, args) = E.Start(parser, argv=argv)

    if len(args) != 2:
        raise ValueError("two arguments required")

    if args[0] == "-":
        infile1 = options.stdin
    else:
        infile1 = IOTools.openFile(args[0], "r")

    infile2 = IOTools.openFile(args[1], "r")

    idx = Bed.readAndIndex(infile2, with_values=True)

    output = options.output
    outfile = options.stdout

    if output == "name":
        outfile.write("name1\tname2\n")
        outf = lambda x: x.fields[0]
    else:
        outf = str

    for bed in Bed.iterator(infile1):
        try:
            overlaps = idx[bed.contig].find(bed.start, bed.end)
        except (KeyError, IndexError):
            # ignore missing contig and zero length intervals
            continue

        for o in overlaps:
            outfile.write("\t".join((outf(bed), outf(o[2]))) + "\n")

    E.Stop()


if __name__ == "__main__":
    sys.exit(main(sys.argv))
########################################################################## # #   MRC FGU Computational Genomics Group # #   $Id: bed2graph.py 2861 2010-02-23 17:36:32Z andreas $ # #   Copyright (C) 2009 <NAME> # #   This program is free software; you can redistribute it and/or #   modify it under the terms of the GNU General Public License #   as published by the Free Software Foundation; either version 2 #   of the License, or (at your option) any later version. # #   This program is distributed in the hope that it will be useful, #   but WITHOUT ANY WARRANTY; without even the implied warranty of #   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the #   GNU General Public License for more details. # #   You should have received a copy of the GNU General Public License #   along with this program; if not, write to the Free Software #   Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA. ########################################################################## bed2graph.py - compute the overlap graph between two bed files ==============================================================  :Author: <NAME> :Release: $Id: bed2graph.py 2861 2010-02-23 17:36:32Z andreas $ :Date: |today| :Tags: Python  Purpose -------  This script ouputs a list of the names of all overlapping intervals  between two bed files.  Usage -----  Type::     python bed2graph.py A.bed.gz B.bed.gz > graph.out  for command line help.  Command line options -------------------- script main.      parses command line options in sys.argv, unless *argv* is given. # setup command line parser # add common options (-h/--help, ...) and parse command line # ignore missing contig and zero length intervals