gencodegenes 1.1.6__tar.gz → 1.1.7__tar.gz

{gencodegenes-1.1.6 → gencodegenes-1.1.7}/MANIFEST.in

@@ -5,6 +5,8 @@ include src/gencodegenes/*.cpp
 include src/gencodegenes/*.py
 include src/gencodegenes/*.pyx
 include src/gencodegenes/*.pxd
+include src/gencodegenes/*.pyi
+include src/gencodegenes/py.typed
 include src/*.h
 include src/*.cpp
 include src/gzstream/gzstream.C

{gencodegenes-1.1.6/src/gencodegenes.egg-info → gencodegenes-1.1.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gencodegenes
-Version: 1.1.6
+Version: 1.1.7
 Summary: Package to load genes from GENCODE GTF files
 Author-email: Jeremy McRae <jeremy.mcrae@gmail.com>
 Project-URL: homepage, https://github.com/jeremymcrae/gencodegenes

{gencodegenes-1.1.6 → gencodegenes-1.1.7}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = 'gencodegenes'
-version = '1.1.6'
+version = '1.1.7'
 description = 'Package to load genes from GENCODE GTF files'
 readme = 'README.md'
 requires-python = ">=3.8"

{gencodegenes-1.1.6 → gencodegenes-1.1.7}/setup.py

@@ -110,7 +110,8 @@ shutil.copy("src/tx.cpp", "src/gencodegenes/tx.cpp")
 
 setup(
     package_dir={'': 'src'},
-    package_data={'gencodegenes': ['transcript.pxd', 'tx.h', 'tx.cpp']},
+    package_data={'gencodegenes': ['transcript.pxd', 'tx.h', 'tx.cpp',
+        'py.typed', '*.pyi']},
     include_package_data=True,
     ext_modules=cythonize(extensions),
     test_suite="tests")

{gencodegenes-1.1.6 → gencodegenes-1.1.7}/src/gencode.cpp

@@ -113,7 +113,7 @@ static void load_transcripts(std::vector<NamedTx> & transcripts, GTF &gtf_file,
             // adjust CDS for start and stop codon coords
             include_end_codons(cds_range, info);
             Tx tx = Tx(info.name, info.chrom, info.start, info.end, info.strand[0], 
-                info.transcript_type);
+                info.transcript_type, info.attributes);
             tx.set_exons(info.exons);
             tx.set_cds(info.cds);
             transcripts.push_back({symbol, alt_ids, tx, info.is_canonical});
@@ -137,6 +137,7 @@ static void load_transcripts(std::vector<NamedTx> & transcripts, GTF &gtf_file,
         if (gtf.feature == "transcript") {
             info.start = gtf.start;
             info.end = gtf.end;
+            info.attributes = std::move(gtf.attributes);
         } else if (gtf.feature == "CDS") {
             info.cds.push_back(std::vector<int> {gtf.start, gtf.end});
             cds_range["max"] = std::max(std::max(cds_range["max"], gtf.start), gtf.end);
@@ -152,7 +153,7 @@ static void load_transcripts(std::vector<NamedTx> & transcripts, GTF &gtf_file,
     // also include the final transcript (if it transcript exists)
     if (info.name != "") {
         include_end_codons(cds_range, info);
-        Tx tx = Tx(info.name, info.chrom, info.start, info.end, info.strand[0], info.transcript_type);
+        Tx tx = Tx(info.name, info.chrom, info.start, info.end, info.strand[0], info.transcript_type, info.attributes);
         tx.set_exons(info.exons);
         tx.set_cds(info.cds);
         transcripts.push_back({symbol, alt_ids, tx, info.is_canonical});

{gencodegenes-1.1.6 → gencodegenes-1.1.7}/src/gencode.h

@@ -25,6 +25,7 @@ struct TxInfo {
     std::vector<std::vector<int> > cds;
     int offset = 0;
     int is_canonical = 0;
+    std::map<std::string, std::string> attributes;
 };
 
 // stores HGNC symbol with the transcript, so we can collect transcripts by gene