add __iter__ and rename all_reads

Author: Hang Ji

flatgfa-py/examples/gaf.py

@@ -1,12 +1,14 @@
 import flatgfa
 
-graph = flatgfa.parse("your-gfa-file")
-gaf = "your-gaf-gile"
-gaf_parser = graph.load_gaf(gaf)
-for read in gaf_parser:
-    print(read.name)
-    print(read.sequence())
-    print(read.segment_ranges())
-    for element in read.chunks:
+graph = flatgfa.parse("name-of-GFA-file")
+gaf = "name-of-GAF-file"
+gaf_parser = graph.all_reads(gaf)
+for lines in gaf_parser:
+    print(lines.name)
+    print(lines.sequence())
+    print(lines.segment_ranges())
+    for element in lines:
         print(element.handle)
         print(element.range)
+
+

flatgfa-py/flatgfa.pyi

@@ -65,13 +65,14 @@ class LinkList:
 class ChunkEvent:
     handle: Handle
     range: tuple[int, int]
-    def __sequence__(self) -> None: ...
+    def sequence(self) -> str: ...
 
 class GAFLine:
     name: str
     chunks: list[ChunkEvent]
     def segment_ranges(self) -> str: ...
     def sequence(self) -> str: ...
+    def __iter__(self) -> Iterator[ChunkEvent]: ...
 
 class GAFParser:
     def __iter__(self) -> Iterator[GAFLine]: ...
@@ -84,7 +85,7 @@ class FlatGFA:
     def write_flatgfa(self, filename: str) -> None: ...
     def write_gfa(self, filename: str) -> None: ...
     def depth(self) -> None: ...
-    def load_gaf(self, gaf: str) -> GAFParser: ...
+    def all_reads(self, gaf: str) -> GAFParser: ...
 
 def parse(filename: str) -> FlatGFA: ...
 def load(filename: str) -> FlatGFA: ...

flatgfa-py/src/lib.rs

@@ -131,7 +131,7 @@ impl PyFlatGFA {
         mmap.flush()?;
         Ok(())
     }
-    fn load_gaf(&self, gaf: &str) -> PyGAFParser {
+    fn all_reads(&self, gaf: &str) -> PyGAFParser {
         let gfa = self.0.view();
         let name_map = flatgfa::namemap::NameMap::build(&gfa);
         let gaf_buf = Arc::new(flatgfa::memfile::map_file(gaf));
@@ -497,6 +497,29 @@ impl PyChunkEvent {
     }
 }
 
+#[pyclass]
+struct PyGAFLineIter {
+    chunks: Vec<PyChunkEvent>,
+    index: usize,
+}
+
+#[pymethods]
+impl PyGAFLineIter {
+    fn __iter__(slf: PyRef<Self>) -> PyRef<Self> {
+        slf
+    }
+
+    fn __next__(mut slf: PyRefMut<Self>) -> Option<PyChunkEvent> {
+        if slf.index < slf.chunks.len() {
+            let item = slf.chunks[slf.index].clone();
+            slf.index += 1;
+            Some(item)
+        } else {
+            None
+        }
+    }
+}
+
 #[pyclass]
 #[pyo3(name = "GAFLine", module = "flatgfa")]
 
@@ -532,6 +555,12 @@ impl PyGAFLine {
         }
         res
     }
+    fn __iter__(slf: PyRef<Self>) -> PyGAFLineIter {
+        PyGAFLineIter {
+            chunks: slf.chunks.clone(),
+            index: 0,
+        }
+    }
 }
 struct OwnedGAFParser {
     mmap: Arc<Mmap>,