'''
bed2bed - manipulate bed files
=================================

Purpose
-------

This script provides various methods for merging (by position, by name
or by score), filtering and moving bed formatted intervals and
outputting the results as a bed file

Methods
-------

This script provides several methods, each with a set of options
to control behavoir:

merge
+++++

Merge together overlapping or adjacent intervals. The basic
functionality is similar to bedtools merge, but with some additions:

* Merging by name: specifying the --merge-by-name option will mean
  that only overlaping (or adjacent intervals) with the same value in
  the 4th column of the bed will be merged

* Removing overlapping intervals with inconsistent names: set the
   ``--remove-inconsistent-names`` option.

.. caution::
   Intervals of the same name will only be merged if they
   are consecutive in the bed file.

* Only output merged intervals: By specifiying the --merge-min-intervals=n
  options, only those intervals that were created by merging at least n
  intervals together will be output

Intervals that are close but not overlapping can be merged by setting
--merge-distance to a non-zero value

bins
++++

Merges together overlapping or adjecent intervals only if they have
"similar" scores. Score similarity is assessed by creating a number of
score bins and assigning each interval to a bin. If two adjacent
intervals are in the same bin, the intervals are merged. Note that in
contrast to merge-by-name above, two intervals do not need to be
overlapping or within a certain distance to be merged.

There are several methods to create the bins:

* equal-bases: Bins are created to that they contain the same number of bases.
  Specified by passing "equal-bases" to --binning-method. This is the default.

* equal-intervals: Score bins are create so that each bin contains the
  same number of intervals. Specified by passing "equal-intervals" to
  --binning-method.

* equal-range: Score bins are created so that
  each bin covers the same fraction of the total range of
  scores. Specified by passing "equal-range" to --binning-method.

* bin-edges: Score binds can be specified by manually passing a comma
  seperated list of bin edges to --bin-edges.

The number of bins is specified by the --num-bins options, and the
default is 5.

block
+++++

Creates blocked bed12 outputs from a bed6, where intervals with the
same name are merged together to create a single bed12 entry.

.. Caution:: Input must be sorted so that entries of the same
name are together.

filter-genome
+++++++++++++

Removes intervals that are on unknown contigs or extend off the 3' or
5' end of the contig.  Requires a tab seperated input file to -g which
lists the contigs in the genome, plus their lengths.

sanitize-genome
+++++++++++++++

As above, but instead of removing intervals overlapping the ends of
contigs, truncates them.  Also removes empty intervals.

filter-names
++++++++++++

Output intervals whose names are in list of desired names. Names are
supplied as a file with one name on each line.

shift
+++++

Moves intervals by the specified amount, but will not allow them to be
shifted off the end of contigs. Thus if a shift will shift the start
of end of the contig, the interval is only moved as much as is
possible without doing this.

rename-chr
++++++++++

Renames chromosome names. Source and target names are supplied as a file
with two columns. Examples are available at:
https://github.com/dpryan79/ChromosomeMappings
Note that unmapped chromosomes are dropped from the output file.

Other options
+++++++++++++

-g/--genome-file, -b/--bam-file:
   the filter-genome, sanitize-genome and shift methods require a genome in
   order to ensure they are not placing intervals outside the limits of
   contigs. This genome can be supplied either as a samtools or cgat indexed
   genome, or extracted from the header of a bam file.

Examples
--------

Merge overlapping or adjectent peaks from a CHiP-seq experiment where the
intervals have the same name:

    cat chip-peaks.bed | cgat bed2bed --method=merge --merge-by-name > chip-peaks-merged.bed

Merge adjected ChIP-seq peaks if their scores are in the same quartile of
all scores:

    cat chip-peaks.bed | cgat bed2bed --method=bins --binning-method=equal-intervals --num-bins=4

Remove intervals that overlap the ends of a contig and those that are on a
non-standard contig. Take the input intervals from a file rather than stdin.
Note that hg19.fasta has been indexed with `index_genome`:

    cgat bed2bed --method=filter-genome --genome-file=hg19.fasta -I chip-peaks.bed -O chip-peaks-sanitized.bed

Convert a bed file contain gene structures with one line per exon to a bed12
with linked block representing the gene structure. Note the transparent use
of compressed input and output files:

    cgat bed2bed --method=block -I transcripts.bed.gz -O transcripts.blocked.bed.gz

Rename UCSC chromosomes to ENSEMBL.

    cat ucsc.bed | cgat bed2bed --method=rename-chr --rename-chr-file=ucsc2ensembl.txt > ensembl.bed

Usage
-----

   cgat bed2bed --method=[METHOD] [OPTIONS]

Will read bed file from stdin and apply the specified method

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

import sys
import cgatcore.experiment as E
import cgat.IndexedFasta as IndexedFasta
import cgat.Bed as Bed
import cgat.Intervals as Intervals
from collections import defaultdict as defaultdict
import pysam
import csv


def filterNames(iterator, names):
    """ Select only those intervals whose name is in names """

    for bed in iterator:
        if bed.name in names:
            yield bed


def merge(iterator,
          max_distance=0,
          by_name=False,
          min_intervals=1,
          remove_inconsistent=False,
          resolve_blocks=False,
          stranded=False):
    """iterator for merging adjacent bed entries.

    *max_distance* > 0 permits merging of intervals that are
    not directly adjacent.

    If *by_name = True*, only entries with the same name are merged.

    If *remove_inconsistent*, overlapping intervals where the names
    are inconsistent will be removed.

    The score gives the number of intervals that have been merged.
    """

    if remove_inconsistent and by_name:
        assert ValueError(
            "using both remove_inconsistent and by_name makes no sense")

    def iterate_chunks(iterator):
        max_end = defaultdict(int)
        to_join = defaultdict(list)
        last_name = defaultdict(str)

        last = next(iterator)

        if not stranded:
            strand = "."
        else:
            strand = last.strand

        max_end[strand] = last.end
        to_join[strand] = [last]

        for bed in iterator:

            if not stranded:
                strand = "."
            else:
                strand = bed.strand

            d = bed.start - max_end[strand]

            if bed.contig == last.contig:
                assert bed.start >= last.start, \
                    "input file should be sorted by contig and position: d=%i:\n%s\n%s\n" \
                    % (d, last, bed)

            if bed.contig != last.contig:

                for s in to_join:
                    if to_join[s]:
                        yield to_join[s]
                    to_join[s] = []
                    max_end[s] = 0

            elif (d > max_distance or
                  (by_name and last_name[strand] and last_name[strand] != bed.name)):

                if to_join[strand]:
                    yield to_join[strand]

                to_join[strand] = list()

            last = bed
            last_name[strand] = last.name
            max_end[strand] = max(bed.end, max_end[strand])
            to_join[strand].append(bed)

        for strand in sorted(to_join):
            if to_join[strand]:
                yield to_join[strand]
        raise StopIteration

    c = E.Counter()

    for to_join in iterate_chunks(iterator):

        c.input += 1

        if remove_inconsistent:
            names = set([x.name for x in to_join])
            if len(names) > 1:
                c.skipped_inconsistent_intervals += 1
                continue

        if resolve_blocks:
            # keep track of number of intervals in each entry
            for bed in to_join:
                bed["score"] = 1
            merged = True
            while merged:
                joined = []
                not_joined = []
                merged = False

                while len(to_join) > 0:
                    bed1, to_join = to_join[0], to_join[1:]
                    intervals1 = bed1.toIntervals()
                    for bed2 in to_join:
                        intervals2 = bed2.toIntervals()
                        if Intervals.calculateOverlap(intervals1, intervals2) > 0:
                            intervals = Intervals.combine(intervals1 +
                                                          intervals2)
                            bed1.fromIntervals(intervals)
                            bed1["score"] += bed2["score"]
                            merged = True
                        else:
                            not_joined.append(bed2)

                    joined.append(bed1)
                    to_join = not_joined
                    not_joined = []

                to_join = joined
                joined = []

            to_join = sorted(to_join, key=lambda x: int(x.start))

            # keep only those with the created from the merge of the minimum
            # number of intervals

            for bed in to_join:

                if bed["score"] < min_intervals:
                    c.skipped_min_intervals += 1
                    continue

                yield bed
                c.output += 1
        else:

            if len(to_join) < min_intervals:
                c.skipped_min_intervals += 1
                continue

            a = to_join[0]
            a.end = max([entry.end for entry in to_join])
            a.score = len(to_join)
            yield a
            c.output += 1

    E.info(str(c))


def filterGenome(iterator, contigs):
    """remove bed intervals that are outside of contigs.

    contigs is a dictionary of contig sizes."""

    ninput, noutput = 0, 0
    nskipped_contig, nskipped_range, nskipped_endzero = 0, 0, 0

    for bed in iterator:
        ninput += 1
        if bed.contig not in contigs:
            nskipped_contig += 1
            continue
        # IMS: add filtering for filtering <0 co-ordinates
        if bed.start < 0 or bed.end < 0:
            nskipped_range += 1
            continue
        # should this not be just >, as co-ordinates are half-closed, so
        # if end = contigs[bed.contig], then interval ends on last base?
        if bed.end > contigs[bed.contig]:
            nskipped_range += 1
            continue
        if bed.end == 0:
            nskipped_endzero += 1
            continue
        noutput += 1
        yield bed

    E.info("ninput=%i, noutput=%i, nskipped_contig=%i, nskipped_range=%i, nskipped_endzero=%i" %
           (ninput, noutput, nskipped_contig, nskipped_range, nskipped_endzero))


def sanitizeGenome(iterator, contigs):
    """truncate bed intervals that extend beyond contigs.

    removes empty intervals (start == end).

    throws an error if start > end.
    """

    ninput, noutput = 0, 0
    ntruncated_contig, nskipped_contig, nskipped_empty = 0, 0, 0

    for bed in iterator:
        ninput += 1
        if bed.contig not in contigs:
            nskipped_contig += 1
            continue
        # IMS: changing >= to > in if statement: next line sets bed.end = contigs[bed.contig]
        # this shouldn't count as a truncation.
        if bed.end > contigs[bed.contig]:
            bed.end = contigs[bed.contig]
            ntruncated_contig += 1
        if bed.start < 0:
            bed.start = 0
            ntruncated_contig += 1
        if bed.start == bed.end:
            nskipped_empty += 1
            continue
        elif bed.start > bed.end:
            raise ValueError("invalid interval: start > end for %s" % str(bed))

        noutput += 1
        yield bed

    E.info("ninput=%i, noutput=%i, nskipped_contig=%i, ntruncated=%i, nskipped_empty=%i" %
           (ninput, noutput, nskipped_contig, ntruncated_contig, nskipped_empty))


def shiftIntervals(iterator, contigs, offset):
    """shift intervals by a certain offset and ensure size is maintaned even id contig end reached.

    contigs is a dictionary of contig sizes."""

    ninput, noutput = 0, 0
    nskipped_contig, nskipped_range = 0, 0

    for bed in iterator:
        ninput += 1
        if bed.contig not in contigs:
            nskipped_contig += 1
            continue
        # IMS: if we skip intervals off the end of the contig we should skipp ones
        # off the start as well
        if bed.start < 0 or bed.end < 0:
            nskipped_range += 1
            continue
        # IMS: changing >= to > as bed is half-open
        if bed.end > contigs[bed.contig]:
            nskipped_range += 1
            continue
        noutput += 1

        # add offset to each start and end, and adjust for contig length
        l = bed.end - bed.start
        newstart = bed.start + offset
        newend = bed.end + offset
        if newstart < 0:
            newstart = 0
            newend = l
        if newend > contigs[bed.contig]:
            newstart = contigs[bed.contig] - l
            newend = contigs[bed.contig]

        bed.start = newstart
        bed.end = newend

        yield bed

    E.info("ninput=%i, noutput=%i, nskipped_contig=%i, nskipped_range=%i" %
           (ninput, noutput, nskipped_contig, nskipped_range))


def extendInterval(iterator, contigs, distance):

    ninput, noutput, nskipped = 0, 0, 0
    for bed in iterator:
        ninput += 1

        if bed.contig not in contigs:
            nskipped += 1
            continue
        if bed.start < 0 or bed.end < 0:
            nskipped += 1
            continue
        if bed.end > contigs[bed.contig]:
            nskipped += 1
            continue

        newstart = bed.start - distance
        newend = bed.end + distance

        if newstart < 0:
            newstart = 0

        if newend > contigs[bed.contig]:
            newend = contigs[bed.contig]

        bed.start = newstart
        bed.end = newend

        noutput += 1
        yield bed

    E.info("ninput = %i, noutput=%i, nskipped=%i" %
           (ninput, noutput, nskipped))


def renameChromosomes(iterator, chr_map):

    ninput, noutput, nskipped = 0, 0, 0

    for bed in iterator:
        ninput += 1

        if bed.contig in chr_map.keys():
            bed.contig = chr_map[bed.contig]
        else:
            nskipped += 1
            continue

        noutput += 1
        yield bed

    E.info("ninput = %i, noutput=%i, nskipped=%i" %
           (ninput, noutput, nskipped))


def main(argv=sys.argv):

    parser = E.OptionParser(version="%prog version: $Id: bed2bed.py 2861 2010-02-23 17:36:32Z andreas $",
                            usage=globals()["__doc__"])

    # IMS: new method: extend intervals by set amount
    parser.add_option("-m", "--method", dest="methods", type="choice",
                      action="append",
                      choices=("merge", "filter-genome", "bins",
                               "block", "sanitize-genome", "shift", "extend",
                               "filter-names", "rename-chr"),
                      help="method to apply [default=%default]")

    parser.add_option("--num-bins", dest="num_bins", type="int",
                      help="number of bins into which to merge (used for "
                      "method `bins) [default=%default]")

    parser.add_option("--bin-edges", dest="bin_edges", type="string",
                      help="bin_edges for binning method [default=%default]")

    parser.add_option(
        "--binning-method", dest="binning_method", type="choice",
        choices=(
            "equal-bases", "equal-intervals", "equal-range"),
        help="method used for binning (used for method `bins` if no "
        "bin_edges is given) [default=%default]")

    parser.add_option(
        "--merge-distance", dest="merge_distance", type="int",
        help="distance in bases over which to merge that are not "
        "directly adjacent [default=%default]")

    parser.add_option(
        "--merge-min-intervals", dest="merge_min_intervals", type="int",
        help="only output merged intervals that are build from at least "
        "x intervals [default=%default]")

    parser.add_option(
        "--merge-by-name", dest="merge_by_name",
        action="store_true",
        help="only merge intervals with the same name [default=%default]")

    parser.add_option(
        "--merge-and-resolve-blocks", dest="resolve_blocks",
        action="store_true",
        help="When merging bed12 entrys, should blocks be resolved?")

    parser.add_option(
        "--merge-stranded", dest="stranded",
        action="store_true",
        help="Only merge intervals on the same strand")

    parser.add_option(
        "--remove-inconsistent-names", dest="remove_inconsistent_names",
        action="store_true",
        help="when merging, do not output intervals where the names of "
        "overlapping intervals do not match [default=%default]")

    parser.add_option(
        "--offset", dest="offset",  type="int",
        help="offset for shifting intervals [default=%default]")

    parser.add_option("-g", "--genome-file", dest="genome_file", type="string",
                      help="filename with genome.")

    parser.add_option("-b", "--bam-file", dest="bam_file", type="string",
                      help="bam-formatted filename with genome.")

    parser.add_option("--filter-names-file", dest="names", type="string",
                      help="list of names to keep. One per line")

    parser.add_option("--rename-chr-file", dest="rename_chr_file", type="string",
                      help="mapping table between old and new chromosome names."
                      "TAB separated 2-column file.")

    parser.set_defaults(methods=[],
                        merge_distance=0,
                        binning_method="equal-bases",
                        merge_by_name=False,
                        genome_file=None,
                        rename_chr_file=None,
                        bam_file=None,
                        num_bins=5,
                        merge_min_intervals=1,
                        bin_edges=None,
                        offset=10000,
                        test=None,
                        extend_distance=1000,
                        remove_inconsistent_names=False,
                        resolve_blocks=False)

    (options, args) = E.start(parser, add_pipe_options=True)

    contigs = None
    chr_map = None

    # Why provide full indexed genome, when a tsv of contig sizes would do?
    if options.genome_file:
        genome_fasta = IndexedFasta.IndexedFasta(options.genome_file)
        contigs = genome_fasta.getContigSizes()

    if options.bam_file:
        samfile = pysam.AlignmentFile(options.bam_file)
        contigs = dict(list(zip(samfile.references, samfile.lengths)))

    if options.rename_chr_file:
        chr_map = {}
        with open(options.rename_chr_file, 'r') as filein:
            reader = csv.reader(filein, delimiter='\t')
            for row in reader:
                if len(row) != 2:
                    raise ValueError("Mapping table must have exactly two columns")
                chr_map[row[0]] = row[1]
        if not len(chr_map.keys()) > 0:
            raise ValueError("Empty mapping dictionnary")

    processor = Bed.iterator(options.stdin)

    for method in options.methods:
        if method == "filter-genome":
            if not contigs:
                raise ValueError("please supply contig sizes")
            processor = filterGenome(processor, contigs)
        elif method == "sanitize-genome":
            if not contigs:
                raise ValueError("please supply contig sizes")
            processor = sanitizeGenome(processor, contigs)
        elif method == "merge":
            processor = merge(
                processor,
                options.merge_distance,
                by_name=options.merge_by_name,
                min_intervals=options.merge_min_intervals,
                remove_inconsistent=options.remove_inconsistent_names,
                resolve_blocks=options.resolve_blocks,
                stranded=options.stranded)
        elif method == "bins":
            if options.bin_edges:
                bin_edges = list(map(float, options.bin_edges.split(",")))
                # IMS: check bin edges are valid
                if not(len(bin_edges) == options.num_bins + 1):
                    raise ValueError(
                        "Number of bin edge must be one more than "
                        "number of bins")
            else:
                bin_edges = None
            processor, bin_edges = Bed.binIntervals(
                processor,
                num_bins=options.num_bins,
                method=options.binning_method,
                bin_edges=bin_edges)
            E.info("# split bed: bin_edges=%s" % (str(bin_edges)))

        elif method == "block":
            processor = Bed.blocked_iterator(processor)
        elif method == "shift":
            # IMS: test that contig sizes are availible
            if not contigs:
                raise ValueError("please supply genome file")
            processor = shiftIntervals(
                processor, contigs, offset=options.offset)
        # IMS: new method: extend intervals by set amount
        elif method == "extend":
            if not contigs:
                raise ValueError("please supply genome file")
            processor = extendInterval(processor, contigs, options.offset)
        elif method == "filter-names":
            if not options.names:
                raise ValueError("please supply list of names to filter")
            names = [name.strip() for name in open(options.names)]
            processor = filterNames(processor, names)
        elif method == "rename-chr":
            if not chr_map:
                raise ValueError("please supply mapping file")
            processor = renameChromosomes(processor, chr_map)

    noutput = 0
    for bed in processor:
        options.stdout.write(str(bed) + "\n")
        noutput += 1

    E.info("noutput=%i" % (noutput))

    E.stop()

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