--- a
+++ b/singlecellmultiomics/features/exonGTFtoIntronGTF.py
@@ -0,0 +1,135 @@
+#!/usr/bin/env python3
+import collections
+import os
+import sys
+import glob
+import argparse
+import itertools
+import gzip
+
+
+def decodeKvPairs(kv):
+    keyValues = {}
+    for part in kv.split(';'):
+        kv = part.strip().split()
+        if len(kv) == 2:
+            key = kv[0]
+            value = kv[1].replace('"', '')
+            keyValues[key] = value
+    return keyValues
+
+
+def exonGTF_to_intronGTF(exon_path, id):
+    # (gene,chrom,strand)-> [range(start,end), range(start,end)]
+    geneToExonRanges = collections.defaultdict(list)
+    prevChrom = None
+    capture = list(set(['gene_id',
+                        'gene_version',
+                        'transcript_version',
+                        'gene_name',
+                        'gene_source',
+                        'gene_biotype',
+                        'transcript_name',
+                        'transcript_source',
+                        'transcript_biotype',
+                        'transcript_support_level']) - set([id]))
+    print(capture)
+
+    id_to_features = {}
+
+    with gzip.open(exon_path, 'rt') if exon_path.endswith('.gz') else open(exon_path) as f:
+        for line in f:
+            if line.startswith('#'):
+                yield line
+                continue
+            chromosome, source, feature_type, feature_start, feature_end, at5, strand, at7, kv = line.split(
+                None, 8)
+
+            if feature_type != 'exon':
+                continue
+
+            meta = decodeKvPairs(kv)
+            id_to_features[meta[id]] = {
+                c: meta.get(c) for c in capture if c in meta
+            }
+            geneToExonRanges[(
+                meta[id], chromosome, strand, source
+            )
+            ].append(range(int(feature_start), int(feature_end) + 1))
+
+            if prevChrom is not None and prevChrom != chromosome:
+                for intr in generate_introns(
+                        geneToExonRanges, id, id_to_features):
+                    yield intr
+                geneToExonRanges = collections.defaultdict(list)
+
+            prevChrom = chromosome
+
+    if prevChrom is not None:
+        for intr in generate_introns(geneToExonRanges, id, id_to_features):
+            yield intr
+        geneToExonRanges = collections.defaultdict(list)
+
+
+def generate_introns(geneToExonRanges, id, id_to_features):
+    for g in geneToExonRanges:
+        if len(geneToExonRanges[g]) == 0:
+            continue
+        geneStart = min([min(r) for r in geneToExonRanges[g]])
+        geneEnd = max([max(r) for r in geneToExonRanges[g]])
+        gene_identifier_or_other, chromosome, strand, source = g
+
+        introns = []
+        in_intron = None
+        current_intron_start = None
+        rest_data = id_to_features.get(gene_identifier_or_other, {})
+
+        if len(rest_data) > 0:
+            rest = '; '.join(
+                [f'{key} {value}' for key, value in rest_data.items()])
+        else:
+            rest = ''
+
+        for i in sorted(
+
+            [geneStart, geneEnd] +
+            [i.start for i in geneToExonRanges[g]] +
+                [i.stop for i in geneToExonRanges[g]]):
+            if any([i in r for r in geneToExonRanges[g]]):
+                if current_intron_start is not None and in_intron is True:
+                    introns.append([current_intron_start, i])
+
+                    yield '\t'.join([str(x) for x in [
+                        chromosome,
+                        source,
+                        'intron',
+                        current_intron_start,
+                        i - 1,
+                        '.',
+                        strand,
+                        '.', f'{id} "{gene_identifier_or_other}";{rest}']]) + '\n'
+
+                in_intron = False
+            else:
+                if in_intron is False:
+                    in_intron = True
+                    current_intron_start = i
+
+
+if __name__ == '__main__':
+    argparser = argparse.ArgumentParser(
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        description="Convert exonic GTF file to intronic GTF file")
+    argparser.add_argument('gffin')
+    argparser.add_argument('-id', help='identifier', default='transcript_id')
+    argparser.add_argument(
+        '-o',
+        help="Output GTF file",
+        type=str,
+        required=True)
+    args = argparser.parse_args()
+
+    with gzip.open(args.o, 'wt') if args.o.endswith('.gz') else open(args.o, 'w') as o:
+        for intron in exonGTF_to_intronGTF(args.gffin, args.id):
+            if intron is not None:
+                o.write(intron)