MAINT: code formatting

src/gbintk/cli.py

@@ -691,7 +691,11 @@ def visualise(
     )
     logger.info("Running Visualisation for binning and refinement results...")
 
-    from gbintk.support import visualise_result_MEGAHIT, visualise_result_SPAdes, visualise_result_Flye
+    from gbintk.support import (
+        visualise_result_Flye,
+        visualise_result_MEGAHIT,
+        visualise_result_SPAdes,
+    )
 
     # Make args class
     class VizArgsObj:

src/gbintk/support/evaluate.py

@@ -64,7 +64,7 @@ def run(args):
 
     all_ground_truth_bins_list = []
 
-    with open(ground_truth_file) as csvfile:
+    with open(ground_truth_file, mode="r") as csvfile:
         readCSV = csv.reader(csvfile, delimiter=delimiter)
         for row in readCSV:
             all_ground_truth_bins_list.append(row[1])
@@ -81,7 +81,7 @@ def run(args):
     ground_truth_count = 0
     ground_truth_bins_1 = {}
 
-    with open(ground_truth_file) as contig_bins:
+    with open(ground_truth_file, mode="r") as contig_bins:
         readCSV = csv.reader(contig_bins, delimiter=delimiter)
 
         for row in readCSV:
@@ -101,7 +101,7 @@ def run(args):
 
     all_bins_list = []
 
-    with open(binned_file) as csvfile:
+    with open(binned_file, mode="r") as csvfile:
         readCSV = csv.reader(csvfile, delimiter=delimiter)
 
         for row in readCSV:
@@ -121,7 +121,7 @@ def run(args):
     binned_count = 0
     binned_contigs = []
 
-    with open(binned_file) as contig_bins:
+    with open(binned_file, mode="r") as contig_bins:
         readCSV = csv.reader(contig_bins, delimiter=delimiter)
         for row in readCSV:
             binned_count += 1

src/gbintk/support/visualise_result_Flye.py

@@ -98,7 +98,6 @@ def run(args):
     logger.info(f"Size of the margin: {margin} pt")
     logger.info(f"Delimiter: {delimiter}")
 
-
     # Get the number of bins from the initial binning result
     # ---------------------------------------------------
 
@@ -124,7 +123,6 @@ def run(args):
         logger.info("Exiting visualiser... Bye...!")
         sys.exit(1)
 
-
     logger.info("Constructing the assembly graph...")
 
     # Get contig names
@@ -303,7 +301,6 @@ def run(args):
 
     logger.info(f"Total number of edges in the assembly graph: {len(edge_list)}")
 
-
     # Get initial binning result
     # ----------------------------
 
@@ -330,7 +327,6 @@ def run(args):
         logger.info("Exiting visualiser... Bye...!")
         sys.exit(1)
 
-
     # Get list of colours according to number of bins
     # -------------------------------------------------
 
@@ -361,11 +357,12 @@ def run(args):
         "#000000",
     ]
 
-
     # Visualise the initial assembly graph
     # --------------------------------------
 
-    logger.info("Drawing and saving the assembly graph with the initial binning result...")
+    logger.info(
+        "Drawing and saving the assembly graph with the initial binning result..."
+    )
 
     initial_out_fig_name = f"{output_path}{prefix}initial_binning_result.{image_type}"
 
@@ -405,7 +402,6 @@ def run(args):
     # Plot the graph
     plot(assembly_graph, initial_out_fig_name, **visual_style)
 
-
     # Get the final GraphBin binning result
     # ---------------------------------------
 
@@ -432,15 +428,16 @@ def run(args):
         logger.info("Exiting visualiseResult... Bye...!")
         sys.exit(1)
 
-
     # Visualise the final assembly graph
     # ------------------------------------
 
     print(
         "Drawing and saving the assembly graph with the final GraphBin binning result..."
     )
 
-    final_out_fig_name = f"{output_path}{prefix}final_GraphBin_binning_result.{image_type}"
+    final_out_fig_name = (
+        f"{output_path}{prefix}final_GraphBin_binning_result.{image_type}"
+    )
 
     node_colours = []
 

src/gbintk/support/visualise_result_MEGAHIT.py

@@ -105,7 +105,7 @@ def run(args):
         all_bins_list = []
         n_bins = 0
 
-        with open(initial_binning_result) as csvfile:
+        with open(initial_binning_result, mode="r") as csvfile:
             readCSV = csv.reader(csvfile, delimiter=delimiter)
             for row in readCSV:
                 all_bins_list.append(row[1])
@@ -149,7 +149,7 @@ def run(args):
 
     try:
         # Get links from .gfa file
-        with open(assembly_graph_file) as file:
+        with open(assembly_graph_file, mode="r") as file:
             for line in file.readlines():
                 line = line.strip()
 
@@ -248,7 +248,7 @@ def run(args):
     bins = [[] for x in range(n_bins)]
 
     try:
-        with open(initial_binning_result) as contig_bins:
+        with open(initial_binning_result, mode="r") as contig_bins:
             readCSV = csv.reader(contig_bins, delimiter=delimiter)
             for row in readCSV:
                 contig_num = contigs_map_rev[int(graph_to_contig_map_rev[row[0]])]
@@ -353,7 +353,7 @@ def run(args):
     bins = [[] for x in range(n_bins)]
 
     try:
-        with open(final_binning_result) as contig_bins:
+        with open(final_binning_result, mode="r") as contig_bins:
             readCSV = csv.reader(contig_bins, delimiter=delimiter)
             for row in readCSV:
                 contig_num = contigs_map_rev[int(graph_to_contig_map_rev[row[0]])]

src/gbintk/support/visualise_result_SPAdes.py

@@ -106,7 +106,7 @@ def run(args):
         all_bins_list = []
         n_bins = 0
 
-        with open(initial_binning_result) as csvfile:
+        with open(initial_binning_result, mode="r") as csvfile:
             readCSV = csv.reader(csvfile, delimiter=delimiter)
             for row in readCSV:
                 all_bins_list.append(row[1])
@@ -137,7 +137,7 @@ def run(args):
     current_contig_num = ""
 
     try:
-        with open(contig_paths) as file:
+        with open(contig_paths, mode="r") as file:
             name = file.readline()
             path = file.readline()
 
@@ -189,7 +189,7 @@ def run(args):
 
     try:
         # Get links from assembly_graph_with_scaffolds.gfa
-        with open(assembly_graph_file) as file:
+        with open(assembly_graph_file, mode="r") as file:
             for line in file.readlines():
                 line = line.strip()
 
@@ -272,7 +272,7 @@ def run(args):
     try:
         all_bins_list = []
 
-        with open(initial_binning_result) as csvfile:
+        with open(initial_binning_result, mode="r") as csvfile:
             readCSV = csv.reader(csvfile, delimiter=delimiter)
             for row in readCSV:
                 all_bins_list.append(row[1])
@@ -297,7 +297,7 @@ def run(args):
     bins = [[] for x in range(n_bins)]
 
     try:
-        with open(initial_binning_result) as contig_bins:
+        with open(initial_binning_result, mode="r") as contig_bins:
             readCSV = csv.reader(contig_bins, delimiter=delimiter)
             for row in readCSV:
                 start = "NODE_"
@@ -402,7 +402,7 @@ def run(args):
     bins = [[] for x in range(n_bins)]
 
     try:
-        with open(final_binning_result) as contig_bins:
+        with open(final_binning_result, mode="r") as contig_bins:
             readCSV = csv.reader(contig_bins, delimiter=delimiter)
             for row in readCSV:
                 if row[1] != "unbinned":