Implemented API

Author: micknudsen

README.md

@@ -51,6 +51,48 @@ gcnvplot plot \
   --output plot.svg
 ```
 
+## Python API
+
+`gcnvplot` can also be used from Python code, for example when generating reports. Use `TranscriptIndex` to keep the SQLite transcript database open while rendering multiple plots.
+
+Use `render_plot_svg` when you want the SVG as a string, for example for embedding the plot directly into an HTML report or notebook:
+
+```python
+from pathlib import Path
+
+import gcnvplot
+
+with gcnvplot.TranscriptIndex(Path("annotations.sqlite")) as transcript_index:
+    svg = gcnvplot.render_plot_svg(
+        Path("sample.tsv"),
+        Path("background.tsv"),
+        transcript_id="NM_007294.4",
+        transcript_index=transcript_index,
+        sample_name="SAMPLE_01",
+        highlight="chr17:43070928-43076614",
+    )
+```
+
+
+Use `write_plot` when you just want the finished SVG saved to disk. It is a convenience wrapper around `render_plot_svg`.
+
+```python
+from pathlib import Path
+
+import gcnvplot
+
+with gcnvplot.TranscriptIndex(Path("annotations.sqlite")) as transcript_index:
+    gcnvplot.write_plot(
+        Path("sample.tsv"),
+        Path("background.tsv"),
+        Path("plot.svg"),
+        transcript_id="NM_007294.4",
+        transcript_index=transcript_index,
+        sample_name="SAMPLE_01",
+        highlight="chr17:43070928-43076614",
+    )
+```
+
 ## Synthetic example
 
 A tiny synthetic BRCA1 transcript example is available in [`examples/brca1_synthetic`](examples/brca1_synthetic). It demonstrates a highlighted multi-exon deletion, filled and open sample dots, and an uncovered-exon marker.

src/gcnvplot/__init__.py

@@ -1,3 +1,32 @@
 """Top-level package for gcnvplot."""
 
+from .core import (
+    BackgroundSummary,
+    Interval,
+    TranscriptAnnotation,
+    TranscriptExon,
+    TranscriptIndex,
+    index_gtf,
+    load_background,
+    parse_read_counts,
+    parse_region,
+    render_plot_svg,
+    write_plot,
+)
+
 __version__ = "0.4.0"
+
+__all__ = [
+    "BackgroundSummary",
+    "Interval",
+    "TranscriptAnnotation",
+    "TranscriptExon",
+    "TranscriptIndex",
+    "__version__",
+    "index_gtf",
+    "load_background",
+    "parse_read_counts",
+    "parse_region",
+    "render_plot_svg",
+    "write_plot",
+]