diff fix-aragorn-gff3.py @ 3:f0f0ab9db43f draft

planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fix-aragorn-gff3.py	Mon Jun 05 02:42:12 2023 +0000
@@ -0,0 +1,68 @@
+#!/usr/bin/env python
+import sys
+import logging
+import argparse
+from CPT_GFFParser import gffParse, gffWrite, gffSeqFeature
+from Bio.SeqFeature import SeqFeature
+from gff3 import feature_lambda, feature_test_type
+
+logging.basicConfig(level=logging.INFO)
+log = logging.getLogger(__name__)
+
+
+def fixed_feature(rec):
+    for idx, feature in enumerate(
+        feature_lambda(
+            rec.features,
+            feature_test_type,
+            {"types": ["tRNA", "tmRNA"]},
+            subfeatures=True,
+        )
+    ):
+
+        fid = "%s-%03d" % (feature.type, 1 + idx)
+        try:
+            name = [feature.type + "-" + feature.qualifiers["Codon"][0]]
+        except KeyError:
+            name = [feature.qualifiers["product"][0]]
+        try:
+            origSource = feature.qualifiers["source"][0]
+        except:
+            origSource = "."
+        gene = gffSeqFeature(
+            location=feature.location,
+            type="gene",
+            qualifiers={"ID": [fid + ".gene"], "source": [origSource], "Name": name},
+        )
+        feature.qualifiers["Name"] = name
+        # Below that we have an mRNA
+        exon = gffSeqFeature(
+            location=feature.location,
+            type="exon",
+            qualifiers={"source": [origSource], "ID": ["%s.exon" % fid], "Name": name},
+        )
+        feature.qualifiers["ID"] = [fid]
+        exon.qualifiers["Parent"] = [fid]
+        feature.qualifiers["Parent"] = [fid + ".gene"]
+        # gene -> trna -> exon
+        feature.sub_features = [exon]
+        gene.sub_features = [feature]
+        yield gene
+
+
+def gff_filter(gff3):
+    found_gff = False
+    for rec in gffParse(gff3):
+        found_gff = True
+        rec.features = sorted(list(fixed_feature(rec)), key=lambda x: x.location.start)
+        rec.annotations = {}
+        gffWrite([rec], sys.stdout)
+    if not found_gff:
+        print("##gff-version 3")
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="add parent gene features to CDSs")
+    parser.add_argument("gff3", type=argparse.FileType("r"), help="GFF3 annotations")
+    args = parser.parse_args()
+    gff_filter(**vars(args))