GIT: Merge branch 'main' of https://github.com/Vini2/gbintk

README.md

@@ -1,6 +1,8 @@
 # GraphBin-Tk: Assembly graph-based metagenomic binning toolkit
 
+![GitHub License](https://img.shields.io/github/license/metagentools/gbintk)
 [![CI](https://github.com/metagentools/gbintk/actions/workflows/testing_python_app.yml/badge.svg)](https://github.com/metagentools/gbintk/actions/workflows/testing_python_app.yml)
+[![codecov](https://codecov.io/gh/metagentools/gbintk/graph/badge.svg?token=r5sniGexZG)](https://codecov.io/gh/metagentools/gbintk)
 [![CodeQL](https://github.com/metagentools/gbintk/actions/workflows/codeql.yml/badge.svg)](https://github.com/metagentools/gbintk/actions/workflows/codeql.yml)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 

pyproject.toml

@@ -16,7 +16,8 @@ dependencies = ["click",
   "scipy",
   "numpy",
   "pandas",
-  "tqdm"]
+  "tqdm",
+  "graphbin"]
 classifiers = [
         "Development Status :: 3 - Alpha",
         "Intended Audience :: Science/Research",

src/gbintk/cli.py

@@ -157,7 +157,68 @@ def graphbin(
     """GraphBin: Refined Binning of Metagenomic Contigs using Assembly Graphs"""
 
     print("Run GraphBin...")
+    from graphbin.utils import (
+        graphbin_Canu,
+        graphbin_Flye,
+        graphbin_MEGAHIT,
+        graphbin_Miniasm,
+        graphbin_SGA,
+        graphbin_SPAdes,
+    )
 
+    class ArgsObj:
+        def __init__(
+            self,
+            assembler,
+            graph,
+            contigs,
+            paths,
+            binned,
+            output,
+            prefix,
+            max_iteration,
+            diff_threshold,
+            delimiter,
+        ):
+            self.assembler = assembler
+            self.graph = graph
+            self.contigs = contigs
+            self.paths = paths
+            self.binned = binned
+            self.output = output
+            self.prefix = prefix
+            self.max_iteration = max_iteration
+            self.diff_threshold = diff_threshold
+            self.delimiter = delimiter
+
+    # Make args object
+    args = ArgsObj(
+        assembler,
+        graph,
+        contigs,
+        paths,
+        binned,
+        output,
+        prefix,
+        max_iteration,
+        diff_threshold,
+        delimiter,
+    )
+
+    # Run GraphBin
+    # ---------------------------------------------------
+    if assembler.lower() == "canu":
+        graphbin_Canu.main(args)
+    if assembler.lower() == "flye":
+        graphbin_Flye.main(args)
+    if assembler.lower() == "megahit":
+        graphbin_MEGAHIT.main(args)
+    if assembler.lower() == "miniasm":
+        graphbin_Miniasm.main(args)
+    if assembler.lower() == "sga":
+        graphbin_SGA.main(args)
+    if assembler.lower() == "spades":
+        graphbin_SPAdes.main(args)
 
 # Main GraphBin2
 # -------------------------------------------------------------------