--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gffcompare_to_bed.py	Thu Jan 11 11:16:51 2018 -0500
@@ -0,0 +1,132 @@
+#!/usr/bin/env python
+"""
+#
+#------------------------------------------------------------------------------
+#                         University of Minnesota
+#         Copyright 2017, Regents of the University of Minnesota
+#------------------------------------------------------------------------------
+# Author:
+#
+#  James E Johnson
+#
+#------------------------------------------------------------------------------
+"""
+
+import argparse
+import sys
+
+
+class BedEntry(object):
+    def __init__(self, chrom=None, chromStart=None, chromEnd=None,
+                 name=None, score=None, strand=None,
+                 thickStart=None, thickEnd=None, itemRgb=None,
+                 blockCount=None, blockSizes=None, blockStarts=None):
+        self.chrom = chrom
+        self.chromStart = int(chromStart)
+        self.chromEnd = int(chromEnd)
+        self.name = name
+        self.score = int(score) if score is not None else 0
+        self.strand = '-' if str(strand).startswith('-') else '+'
+        self.thickStart = int(thickStart) if thickStart else self.chromStart
+        self.thickEnd = int(thickEnd) if thickEnd else self.chromEnd
+        self.itemRgb = str(itemRgb) if itemRgb is not None else r'100,100,100'
+        self.blockCount = int(blockCount)
+        if isinstance(blockSizes, str) or isinstance(blockSizes, unicode):
+            self.blockSizes = [int(x) for x in blockSizes.split(',')]
+        elif isinstance(blockSizes, list):
+            self.blockSizes = [int(x) for x in blockSizes]
+        else:
+            self.blockSizes = blockSizes
+        if isinstance(blockStarts, str) or isinstance(blockSizes, unicode):
+            self.blockStarts = [int(x) for x in blockStarts.split(',')]
+        elif isinstance(blockStarts, list):
+            self.blockStarts = [int(x) for x in blockStarts]
+        else:
+            self.blockStarts = blockStarts
+
+    def __str__(self):
+        return '%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s' % (
+            self.chrom, self.chromStart, self.chromEnd,
+            self.name, self.score, self.strand,
+            self.thickStart, self.thickEnd, str(self.itemRgb), self.blockCount,
+            ','.join([str(x) for x in self.blockSizes]),
+            ','.join([str(x) for x in self.blockStarts]))
+
+
+def __main__():
+    parser = argparse.ArgumentParser(
+        description='Retrieve Ensembl cDNAs and three frame translate')
+    parser.add_argument(
+        'input',
+        help='GFFCompare annotated GTF file,  (-) for stdin')
+    parser.add_argument(
+        'output',
+        help='BED file,  (-) for stdout')
+    parser.add_argument(
+        '-C', '--class_code', action='append', default=[],
+        help='Restrict output to gffcompare class codes')
+    parser.add_argument('-d', '--debug', action='store_true', help='Debug')
+    args = parser.parse_args()
+
+    # print >> sys.stderr, "args: %s" % args
+    input_rdr = open(args.input, 'r') if args.input != '-' else sys.stdin
+    output_wtr = open(args.output, 'w') if args.output != '-' else sys.stdout
+
+    def write_bed_entry(bed):
+        if bed.blockCount == 0:
+            bed.blockCount = 1
+        output_wtr.write("%s\n" % str(bed))
+
+    class_codes = [c.strip() for codes in args.class_code
+                   for c in codes.split(',')] if args.class_code else None
+    bed = None
+    class_code = None
+    for i, line in enumerate(input_rdr):
+        if line.startswith('#'):
+            continue
+        fields = line.rstrip('\r\n').split('\t')
+        if len(fields) != 9:
+            continue
+        (seqname, source, feature, start, end,
+         score, strand, frame, attributes) = fields
+        attribute = {i[0]: i[1].strip('"') for i in [j.strip().split(' ')
+                     for j in attributes.rstrip(';').split(';')]}
+        if feature == 'transcript':
+            if args.debug:
+                print >> sys.stderr, "%s\t%s"\
+                    % ('\t'.join([seqname, source, feature,
+                                  start, end, score, strand, frame]),
+                        attribute)
+            if bed is not None:
+                write_bed_entry(bed)
+                bed = None
+            class_code = attribute['class_code'].strip('"')\
+                if 'class_code' in attribute else None
+            if class_codes and class_code not in class_codes:
+                continue
+            chromStart = int(start) - 1
+            chromEnd = int(end)
+            cat = '_' + class_code if class_code and class_code != '=' else ''
+            bed = BedEntry(chrom=seqname,
+                           chromStart=chromStart, chromEnd=chromEnd,
+                           name=attribute['transcript_id'] + cat,
+                           strand=strand,
+                           blockCount=0,
+                           blockSizes=[chromEnd - chromStart],
+                           blockStarts=[0])
+        elif feature == 'exon' and bed is not None:
+            chromStart = int(start) - 1
+            chromEnd = int(end)
+            blockSize = chromEnd - chromStart
+            if bed.blockCount == 0:
+                bed.blockSizes = []
+                bed.blockStarts = []
+            bed.blockSizes.append(blockSize)
+            bed.blockStarts.append(chromStart - bed.chromStart)
+            bed.blockCount += 1
+    if bed is not None:
+        write_bed_entry(bed)
+
+
+if __name__ == "__main__":
+    __main__()