--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gff3_to_json.py	Wed Dec 21 10:02:59 2016 -0500
@@ -0,0 +1,255 @@
+from __future__ import print_function
+
+import json
+import optparse
+import sys
+
+cds_parent_dict = dict()
+exon_parent_dict = dict()
+five_prime_utr_parent_dict = dict()
+gene_count = 0
+gene_dict = dict()
+transcript_dict = dict()
+three_prime_utr_parent_dict = dict()
+
+
+def feature_to_json(cols):
+    d = {
+        'end': int(cols[4]),
+        'start': int(cols[3]),
+    }
+    for attr in cols[8].split(';'):
+        if '=' in attr:
+            (tag, value) = attr.split('=')
+            if tag == 'ID':
+                d['id'] = value
+            else:
+                d[tag] = value
+    if cols[6] == '+':
+        d['strand'] = 1
+    elif cols[6] == '-':
+        d['strand'] = -1
+    else:
+        raise Exception("Unrecognized strand '%s'" % cols[6])
+    return d
+
+
+def gene_to_json(cols, species):
+    global gene_count
+    gene = feature_to_json(cols)
+    gene.update({
+        'member_id': gene_count,
+        'object_type': 'Gene',
+        'seq_region_name': cols[0],
+        'species': species,
+        'Transcript': [],
+    })
+    gene_dict[gene['id']] = gene
+    gene_count = gene_count + 1
+
+
+def transcript_to_json(cols, species):
+    transcript = feature_to_json(cols)
+    transcript.update({
+        'object_type': 'Transcript',
+        'seq_region_name': cols[0],
+        'species': species,
+    })
+    transcript_dict[transcript['id']] = transcript
+
+
+def exon_to_json(cols, species):
+    exon = feature_to_json(cols)
+    exon.update({
+        'length': int(cols[4]) - int(cols[3]) + 1,
+        'object_type': 'Exon',
+        'seq_region_name': cols[0],
+        'species': species,
+    })
+    if 'id' not in exon and 'Name' in exon:
+        exon['id'] = exon['Name']
+
+    if 'Parent' in exon:
+        for parent in exon['Parent'].split(','):
+            if parent not in exon_parent_dict:
+                exon_parent_dict[parent] = [exon]
+            else:
+                exon_parent_dict[parent].append(exon)
+
+
+def five_prime_utr_to_json(cols):
+    five_prime_utr = feature_to_json(cols)
+    if 'Parent' in five_prime_utr:
+        for parent in five_prime_utr['Parent'].split(','):
+            # the 5' UTR can be split among multiple exons
+            if parent not in five_prime_utr_parent_dict:
+                five_prime_utr_parent_dict[parent] = [five_prime_utr]
+            else:
+                five_prime_utr_parent_dict[parent].append(five_prime_utr)
+
+
+def three_prime_utr_to_json(cols):
+    three_prime_utr = feature_to_json(cols)
+    if 'Parent' in three_prime_utr:
+        for parent in three_prime_utr['Parent'].split(','):
+            # the 3' UTR can be split among multiple exons
+            if parent not in three_prime_utr_parent_dict:
+                three_prime_utr_parent_dict[parent] = [three_prime_utr]
+            else:
+                three_prime_utr_parent_dict[parent].append(three_prime_utr)
+
+
+def cds_to_json(cols):
+    cds = feature_to_json(cols)
+    if 'id' not in cds:
+        if 'Name' in cds:
+            cds['id'] = cds['Name']
+        elif 'Parent' in cds:
+            cds['id'] = cds['Parent']
+    if 'Parent' in cds:
+        # At this point we are sure than 'id' is in cds
+        for parent in cds['Parent'].split(','):
+            if parent not in cds_parent_dict:
+                cds_parent_dict[parent] = [cds]
+            else:
+                cds_parent_dict[parent].append(cds)
+
+
+def join_dicts():
+    for parent, exon_list in exon_parent_dict.items():
+        exon_list.sort(key=lambda _: _['start'])
+        if parent in transcript_dict:
+            transcript_dict[parent]['Exon'] = exon_list
+
+    for transcript_id, transcript in transcript_dict.items():
+        translation = {
+            'CDS': [],
+            'id': None,
+            'end': transcript['end'],
+            'object_type': 'Translation',
+            'species': transcript['species'],
+            'start': transcript['start'],
+        }
+        found_cds = False
+        derived_translation_start = None
+        derived_translation_end = None
+        if transcript_id in cds_parent_dict:
+            cds_list = cds_parent_dict[transcript_id]
+            cds_ids = set(_['id'] for _ in cds_list)
+            if len(cds_ids) > 1:
+                raise Exception("Transcript %s has multiple CDSs: this is not supported by Ensembl JSON format" % parent)
+            translation['id'] = cds_ids.pop()
+            cds_list.sort(key=lambda _: _['start'])
+            translation['CDS'] = cds_list
+            translation['start'] = cds_list[0]['start']
+            translation['end'] = cds_list[-1]['end']
+            found_cds = True
+        if transcript_id in five_prime_utr_parent_dict:
+            five_prime_utr_list = five_prime_utr_parent_dict[transcript_id]
+            five_prime_utr_list.sort(key=lambda _: _['start'])
+            if transcript['strand'] == 1:
+                derived_translation_start = five_prime_utr_list[-1]['end'] + 1
+            else:
+                derived_translation_end = five_prime_utr_list[0]['start'] - 1
+        if transcript_id in three_prime_utr_parent_dict:
+            three_prime_utr_list = three_prime_utr_parent_dict[transcript_id]
+            three_prime_utr_list.sort(key=lambda _: _['start'])
+            if transcript['strand'] == 1:
+                derived_translation_end = three_prime_utr_list[0]['start'] - 1
+            else:
+                derived_translation_start = three_prime_utr_list[-1]['end'] + 1
+        if derived_translation_start is not None:
+            if found_cds:
+                if derived_translation_start > translation['start']:
+                    raise Exception("UTR overlaps with CDS")
+            else:
+                translation['start'] = derived_translation_start
+        if derived_translation_end is not None:
+            if found_cds:
+                if derived_translation_end < translation['end']:
+                    raise Exception("UTR overlaps with CDS")
+            else:
+                translation['end'] = derived_translation_end
+        if found_cds or derived_translation_start is not None or derived_translation_end is not None:
+            transcript['Translation'] = translation
+
+    for transcript in transcript_dict.values():
+        if 'Parent' in transcript:
+            # A polycistronic transcript can have multiple parents
+            for parent in transcript['Parent'].split(','):
+                if parent in gene_dict:
+                    gene_dict[parent]['Transcript'].append(transcript)
+
+
+def merge_dicts(json_arg):
+    with open(json_arg) as f:
+        dict_from_json = json.load(f)
+    gene_intersection = set(gene_dict.keys()) & set(dict_from_json.keys())
+    if gene_intersection:
+        raise Exception("JSON file '%s' contains information for genes '%s', which are also present in other files" % (json_arg, ', '.join(gene_intersection)))
+    gene_dict.update(dict_from_json)
+
+
+def write_json(outfile=None, sort_keys=False):
+    if outfile:
+        with open(outfile, 'w') as f:
+            json.dump(gene_dict, f, sort_keys=sort_keys)
+    else:
+        print(json.dumps(gene_dict, indent=3, sort_keys=sort_keys))
+
+
+def __main__():
+    parser = optparse.OptionParser()
+    parser.add_option('--gff3', action='append', default=[], help='GFF3 file to convert, in SPECIES:FILENAME format. Use multiple times to add more files')
+    parser.add_option('--json', action='append', default=[], help='JSON file to merge. Use multiple times to add more files')
+    parser.add_option('-s', '--sort', action='store_true', help='Sort the keys in the JSON output')
+    parser.add_option('-o', '--output', help='Path of the output file. If not specified, will print on the standard output')
+    options, args = parser.parse_args()
+
+    if args:
+        raise Exception('Use options to provide inputs')
+    for gff3_arg in options.gff3:
+        try:
+            (species, filename) = gff3_arg.split(':')
+        except ValueError:
+            raise Exception("Argument for --gff3 '%s' is not in the SPECIES:FILENAME format" % gff3_arg)
+        with open(filename) as f:
+            for i, line in enumerate(f):
+                line = line.strip()
+                if not line:
+                    # skip empty lines
+                    continue
+                if line[0] == '#':
+                    # skip comment lines
+                    continue
+                cols = line.split('\t')
+                if len(cols) != 9:
+                    raise Exception("Line %i in file '%s': '%s' does not have 9 columns" % (i, filename, line))
+                feature_type = cols[2]
+                try:
+                    if feature_type == 'gene':
+                        gene_to_json(cols, species)
+                    elif feature_type in ('mRNA', 'transcript'):
+                        transcript_to_json(cols, species)
+                    elif feature_type == 'exon':
+                        exon_to_json(cols, species)
+                    elif feature_type == 'five_prime_UTR':
+                        five_prime_utr_to_json(cols)
+                    elif feature_type == 'three_prime_UTR':
+                        three_prime_utr_to_json(cols)
+                    elif feature_type == 'CDS':
+                        cds_to_json(cols)
+                    else:
+                        print("Line %i in file '%s': '%s' is not an implemented feature type" % (i, filename, feature_type), file=sys.stderr)
+                except Exception as e:
+                    raise Exception("Line %i in file '%s': %s" % (i, filename, e))
+    join_dicts()
+
+    for json_arg in options.json:
+        merge_dicts(json_arg)
+
+    write_json(options.output, options.sort)
+
+
+if __name__ == '__main__':
+    __main__()