--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/interval2maf.py	Fri Jul 10 16:05:40 2020 -0400
@@ -0,0 +1,145 @@
+#!/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(bx.intervals.io.NiceReaderWrapper(open(interval_file, 'r'), 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__()