--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/interval_maf_to_merged_fasta.py	Fri Jul 24 12:35:57 2020 -0400
@@ -0,0 +1,203 @@
+#!/usr/bin/env python
+"""
+Reads an interval or gene BED and a MAF Source.
+Produces a FASTA file containing the aligned intervals/gene sequences, based upon the provided coordinates
+
+Alignment blocks are layered ontop of each other based upon score.
+
+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
+   -G, --geneBED: Input is a Gene BED file, process and join exons as one region
+   -t, --mafSourceType=t: Type of MAF source to use
+   -m, --mafSource=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
+   -O, --overwrite_with_gaps=O: Overwrite bases found in a lower-scoring block with gaps interior to the sequence for a species.
+   -z, --mafIndexFileDir=z: Directory of local maf_index.loc file
+
+usage: %prog dbkey_of_BED comma_separated_list_of_additional_dbkeys_to_extract comma_separated_list_of_indexed_maf_files input_gene_bed_file output_fasta_file cached|user GALAXY_DATA_INDEX_DIR
+"""
+# Dan Blankenberg
+from __future__ import print_function
+
+import sys
+
+import bx.intervals.io
+from bx.cookbook import doc_optparse
+
+from galaxy.tools.util import maf_utilities
+
+
+def stop_err(msg):
+    sys.exit(msg)
+
+
+def __main__():
+    # Parse Command Line
+    options, args = doc_optparse.parse(__doc__)
+    mincols = 0
+    strand_col = -1
+
+    if options.dbkey:
+        primary_species = options.dbkey
+    else:
+        primary_species = None
+    if primary_species in [None, "?", "None"]:
+        stop_err("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.")
+
+    include_primary = True
+    secondary_species = maf_utilities.parse_species_option(options.species)
+    if secondary_species:
+        species = list(secondary_species)  # make copy of species list
+        if primary_species in secondary_species:
+            secondary_species.remove(primary_species)
+        else:
+            include_primary = False
+    else:
+        species = None
+
+    if options.interval_file:
+        interval_file = options.interval_file
+    else:
+        stop_err("Input interval file has not been specified.")
+
+    if options.output_file:
+        output_file = options.output_file
+    else:
+        stop_err("Output file has not been specified.")
+
+    if not options.geneBED:
+        if options.chromCol:
+            chr_col = int(options.chromCol) - 1
+        else:
+            stop_err("Chromosome column not set, click the pencil icon in the history item to set the metadata attributes.")
+
+        if options.startCol:
+            start_col = int(options.startCol) - 1
+        else:
+            stop_err("Start column not set, click the pencil icon in the history item to set the metadata attributes.")
+
+        if options.endCol:
+            end_col = int(options.endCol) - 1
+        else:
+            stop_err("End column not set, click the pencil icon in the history item to set the metadata attributes.")
+
+        if options.strandCol:
+            strand_col = int(options.strandCol) - 1
+
+    mafIndexFile = "%s/maf_index.loc" % options.mafIndexFileDir
+
+    overwrite_with_gaps = True
+    if options.overwrite_with_gaps and options.overwrite_with_gaps.lower() == 'false':
+        overwrite_with_gaps = False
+
+    # Finish parsing command line
+
+    # get index for mafs based on type
+    index = index_filename = None
+    # using specified uid for locally cached
+    if options.mafSourceType.lower() in ["cached"]:
+        index = maf_utilities.maf_index_by_uid(options.mafSource, mafIndexFile)
+        if index is None:
+            stop_err("The MAF source specified (%s) appears to be invalid." % (options.mafSource))
+    elif options.mafSourceType.lower() in ["user"]:
+        # index maf for use here, need to remove index_file when finished
+        index, index_filename = maf_utilities.open_or_build_maf_index(options.mafSource, options.mafIndex, species=[primary_species])
+        if index is None:
+            stop_err("Your MAF file appears to be malformed.")
+    else:
+        stop_err("Invalid MAF source type specified.")
+
+    # open output file
+    output = open(output_file, "w")
+
+    if options.geneBED:
+        region_enumerator = maf_utilities.line_enumerator(open(interval_file, "r").readlines())
+    else:
+        region_enumerator = enumerate(bx.intervals.io.NiceReaderWrapper(
+            open(interval_file, 'r'), chrom_col=chr_col, start_col=start_col,
+            end_col=end_col, strand_col=strand_col, fix_strand=True,
+            return_header=False, return_comments=False))
+
+    # Step through intervals
+    regions_extracted = 0
+    line_count = 0
+    for line_count, line in region_enumerator:
+        try:
+            if options.geneBED:  # Process as Gene BED
+                try:
+                    starts, ends, fields = maf_utilities.get_starts_ends_fields_from_gene_bed(line)
+                    # create spliced alignment object
+                    alignment = maf_utilities.get_spliced_region_alignment(
+                        index, primary_species, fields[0], starts, ends,
+                        strand='+', species=species, mincols=mincols,
+                        overwrite_with_gaps=overwrite_with_gaps)
+                    primary_name = secondary_name = fields[3]
+                    alignment_strand = fields[5]
+                except Exception as e:
+                    print("Error loading exon positions from input line %i: %s" % (line_count, e))
+                    continue
+            else:  # Process as standard intervals
+                try:
+                    # create spliced alignment object
+                    alignment = maf_utilities.get_region_alignment(
+                        index, primary_species, line.chrom, line.start,
+                        line.end, strand='+', species=species, mincols=mincols,
+                        overwrite_with_gaps=overwrite_with_gaps)
+                    primary_name = "%s(%s):%s-%s" % (line.chrom, line.strand, line.start, line.end)
+                    secondary_name = ""
+                    alignment_strand = line.strand
+                except Exception as e:
+                    print("Error loading region positions from input line %i: %s" % (line_count, e))
+                    continue
+
+            # Write alignment to output file
+            # Output primary species first, if requested
+            if include_primary:
+                output.write(">%s.%s\n" % (primary_species, primary_name))
+                if alignment_strand == "-":
+                    output.write(alignment.get_sequence_reverse_complement(primary_species))
+                else:
+                    output.write(alignment.get_sequence(primary_species))
+                output.write("\n")
+            # Output all remainging species
+            for spec in secondary_species or alignment.get_species_names(skip=primary_species):
+                if secondary_name:
+                    output.write(">%s.%s\n" % (spec, secondary_name))
+                else:
+                    output.write(">%s\n" % (spec))
+                if alignment_strand == "-":
+                    output.write(alignment.get_sequence_reverse_complement(spec))
+                else:
+                    output.write(alignment.get_sequence(spec))
+                output.write("\n")
+
+            output.write("\n")
+            regions_extracted += 1
+        except Exception as e:
+            print("Unexpected error from input line %i: %s" % (line_count, e))
+            raise
+
+    # close output file
+    output.close()
+
+    # remove index file if created during run
+    maf_utilities.remove_temp_index_file(index_filename)
+
+    # Print message about success for user
+    if regions_extracted > 0:
+        print("%i regions were processed successfully." % (regions_extracted))
+    else:
+        print("No regions were processed successfully.")
+        if line_count > 0 and options.geneBED:
+            print("This tool requires your input file to conform to the 12 column BED standard.")
+
+
+if __name__ == "__main__":
+    __main__()