galaxy/tools/maf/interval2maf.py

#!/usr/bin/env python
"""
Reads a list of intervals and a maf. Produces a new maf containing the
blocks or parts of blocks in the original that overlapped the intervals.

If a MAF file, not UID, is provided the MAF file is indexed before being processed.

NOTE: If two intervals overlap the same block it will be written twice.

usage: %prog maf_file [options]
   -d, --dbkey=d: Database key, ie hg17
   -c, --chromCol=c: Column of Chr
   -s, --startCol=s: Column of Start
   -e, --endCol=e: Column of End
   -S, --strandCol=S: Column of Strand
   -t, --mafType=t: Type of MAF source to use
   -m, --mafFile=m: Path of source MAF file, if not using cached version
   -I, --mafIndex=I: Path of precomputed source MAF file index, if not using cached version
   -i, --interval_file=i:       Input interval file
   -o, --output_file=o:      Output MAF file
   -p, --species=p: Species to include in output
   -P, --split_blocks_by_species=P: Split blocks by species
   -r, --remove_all_gap_columns=r: Remove all Gap columns
   -l, --indexLocation=l: Override default maf_index.loc file
   -z, --mafIndexFile=z: Directory of local maf index file ( maf_index.loc or maf_pairwise.loc )
"""
# Dan Blankenberg
from __future__ import print_function

import bx.align.maf
import bx.intervals.io
from bx.cookbook import doc_optparse

from galaxy.tools.util import maf_utilities


def __main__():
    index = index_filename = None

    # Parse Command Line
    options, args = doc_optparse.parse(__doc__)

    if options.dbkey:
        dbkey = options.dbkey
    else:
        dbkey = None
    if dbkey in [None, "?"]:
        maf_utilities.tool_fail(
            "You must specify a proper build in order to extract alignments. You can specify your genome build by clicking on the pencil icon associated with your interval file."
        )

    species = maf_utilities.parse_species_option(options.species)

    if options.chromCol:
        chromCol = int(options.chromCol) - 1
    else:
        maf_utilities.tool_fail(
            "Chromosome column not set, click the pencil icon in the history item to set the metadata attributes."
        )

    if options.startCol:
        startCol = int(options.startCol) - 1
    else:
        maf_utilities.tool_fail(
            "Start column not set, click the pencil icon in the history item to set the metadata attributes."
        )

    if options.endCol:
        endCol = int(options.endCol) - 1
    else:
        maf_utilities.tool_fail(
            "End column not set, click the pencil icon in the history item to set the metadata attributes."
        )

    if options.strandCol:
        strandCol = int(options.strandCol) - 1
    else:
        strandCol = -1

    if options.interval_file:
        interval_file = options.interval_file
    else:
        maf_utilities.tool_fail("Input interval file has not been specified.")

    if options.output_file:
        output_file = options.output_file
    else:
        maf_utilities.tool_fail("Output file has not been specified.")

    split_blocks_by_species = remove_all_gap_columns = False
    if options.split_blocks_by_species and options.split_blocks_by_species == "split_blocks_by_species":
        split_blocks_by_species = True
        if options.remove_all_gap_columns and options.remove_all_gap_columns == "remove_all_gap_columns":
            remove_all_gap_columns = True
    else:
        remove_all_gap_columns = True
    # Finish parsing command line

    # Open indexed access to MAFs
    if options.mafType:
        if options.indexLocation:
            index = maf_utilities.maf_index_by_uid(options.mafType, options.indexLocation)
        else:
            index = maf_utilities.maf_index_by_uid(options.mafType, options.mafIndexFile)
        if index is None:
            maf_utilities.tool_fail("The MAF source specified (%s) appears to be invalid." % (options.mafType))
    elif options.mafFile:
        index, index_filename = maf_utilities.open_or_build_maf_index(
            options.mafFile, options.mafIndex, species=[dbkey]
        )
        if index is None:
            maf_utilities.tool_fail("Your MAF file appears to be malformed.")
    else:
        maf_utilities.tool_fail("Desired source MAF type has not been specified.")

    # Create MAF writter
    out = bx.align.maf.Writer(open(output_file, "w"))

    # Iterate over input regions
    num_blocks = 0
    num_regions = None
    for num_regions, region in enumerate(  # noqa: B007
        bx.intervals.io.NiceReaderWrapper(
            open(interval_file),
            chrom_col=chromCol,
            start_col=startCol,
            end_col=endCol,
            strand_col=strandCol,
            fix_strand=True,
            return_header=False,
            return_comments=False,
        )
    ):
        src = maf_utilities.src_merge(dbkey, region.chrom)
        for block in index.get_as_iterator(src, region.start, region.end):
            if split_blocks_by_species:
                blocks = [
                    new_block
                    for new_block in maf_utilities.iter_blocks_split_by_species(block)
                    if maf_utilities.component_overlaps_region(new_block.get_component_by_src_start(dbkey), region)
                ]
            else:
                blocks = [block]
            for block in blocks:
                block = maf_utilities.chop_block_by_region(block, src, region)
                if block is not None:
                    if species is not None:
                        block = block.limit_to_species(species)
                    block = maf_utilities.orient_block_by_region(block, src, region)
                    if remove_all_gap_columns:
                        block.remove_all_gap_columns()
                    out.write(block)
                    num_blocks += 1

    # Close output MAF
    out.close()

    # remove index file if created during run
    maf_utilities.remove_temp_index_file(index_filename)

    if num_blocks:
        print("%i MAF blocks extracted for %i regions." % (num_blocks, (num_regions + 1)))
    elif num_regions is not None:
        print("No MAF blocks could be extracted for %i regions." % (num_regions + 1))
    else:
        print("No valid regions have been provided.")


if __name__ == "__main__":
    __main__()