Merge pull request #75 from czbiohub-sf/coding-feature-genbank

Coding feature genbank
czbiohub-sf · Jun 5, 2024 · 6ff1e2b · 6ff1e2b
2 parents 20c3ed8 + 12e0186
commit 6ff1e2b
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Showing 2 changed files with 10 additions and 2 deletions.
diff --git a/protoSpaceJAM/_version.py b/protoSpaceJAM/_version.py
@@ -12,5 +12,5 @@
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.dev493+gba78adf.d20240528'
-__version_tuple__ = version_tuple = (0, 1, 'dev493', 'gba78adf.d20240528')
+__version__ = version = '0.1.dev498+g20c3ed8.d20240605'
+__version_tuple__ = version_tuple = (0, 1, 'dev498', 'g20c3ed8.d20240605')
diff --git a/protoSpaceJAM/protoSpaceJAM.py b/protoSpaceJAM/protoSpaceJAM.py
@@ -511,6 +511,7 @@ def main(custom_args=None):
         ENST_design_counts = {} #used to keep track of number of designs for each ENST
         Entry = 0 # Entry is defined by the portal, and if not using the portal, it is just the index of the row
         total_entries = df.shape[0]
+        skipped_count = 0
         for index, row in df.iterrows():
             ENST_ID = row["Ensembl_ID"]
             if isinstance(ENST_ID, str):
@@ -1234,11 +1235,18 @@ def write_genbank(handle, data_obj, donor_name, donor_type):
 
     feature = SeqFeature(FeatureLocation(start=data_obj.Donor_features["tag_coord"][0], end=data_obj.Donor_features["tag_coord"][1], strand=data_obj.Donor_features["HA_payload_strand"]), type='payload', qualifiers={"label": "payload"})
     seq_record.features.append(feature)
+    payload_sequence = sequence[data_obj.Donor_features["tag_coord"][0]:data_obj.Donor_features["tag_coord"][1]]
+    # translate the payload
+    payload_aa_seq = translate_sequence(str(payload_sequence))
+    feature = SeqFeature(FeatureLocation(start=data_obj.Donor_features["tag_coord"][0], end=data_obj.Donor_features["tag_coord"][1], strand=data_obj.Donor_features["HA_payload_strand"]), type='CDS', qualifiers={"label": "CDS", "codon_start":1, "translation": payload_aa_seq})
+    seq_record.features.append(feature)
+
 
     if "coding_coord" in data_obj.Donor_features:
         for feat in data_obj.Donor_features["coding_coord"]:
             feature = SeqFeature(FeatureLocation(start=feat[0], end=feat[1]), strand=data_obj.Donor_features["HA_payload_strand"], type='exon ', qualifiers={"label": "exon"})
             seq_record.features.append(feature)
+
     if "ORF_coord" in data_obj.Donor_features:
         for feat in data_obj.Donor_features["ORF_coord"]:
             #feature = SeqFeature(FeatureLocation(start=feat[0], end=feat[1]), strand=data_obj.Donor_features["HA_payload_strand"], type='CDS-in-frame', qualifiers={"label": "CDS-in-frame"})