Merge pull request #759 from uclahs-cds/czhu-fix-index

GTF source not written to index files
uclahs-cds · Jul 4, 2023 · 8cdca92 · 8cdca92
2 parents f107557 + a523c63
commit 8cdca92
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/moPepGen/cli/generate_index.py b/moPepGen/cli/generate_index.py
@@ -64,7 +64,7 @@ def index_gtf(file:Path, source:str=None, proteome:aa.AminoAcidSeqDict=None,
         anno.check_protein_coding(proteome, invalid_protein_as_noncoding)
 
     gene_idx_file, tx_idx_file = anno.get_index_files(file)
-    metadata = GTFIndexMetadata()
+    metadata = GTFIndexMetadata(source=anno.source)
 
     with open(gene_idx_file, 'wt') as handle:
         metadata.write(handle)

diff --git a/test/files/annotation_gene.idx b/test/files/annotation_gene.idx
@@ -1,8 +1,8 @@
-##source=None
+##source=GENCODE
 ##python=3.8.17
 ##moPepGen=1.1.0
 ##biopython=1.81
-ENSG00000128408.9	0	174	ENST00000614168.2,ENST00000614167.2
+ENSG00000128408.9	0	174	ENST00000614167.2,ENST00000614168.2
 ENSG00000244486.9	12491	12694	ENST00000622235.5
 ENSG00000099949.21	24586	24955	ENST00000642151.1
 ENSG00000279973.2	27280	27432	ENST00000624155.2
diff --git a/test/files/annotation_tx.idx b/test/files/annotation_tx.idx
@@ -1,4 +1,4 @@
-##source=None
+##source=GENCODE
 ##python=3.8.17
 ##moPepGen=1.1.0
 ##biopython=1.81