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MAINT: Refactoring log messages and code formatting
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@Vini2
Vini2 committed Aug 6, 2024
1 parent d657669 commit 7302e31
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Showing 3 changed files with 132 additions and 129 deletions.
87 changes: 44 additions & 43 deletions src/graphbin2/graphbin2_Flye.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,9 @@
import sys
import time

from cogent3.parse.fasta import MinimalFastaParser
from collections import defaultdict

from cogent3.parse.fasta import MinimalFastaParser
from igraph import *
from tqdm import tqdm

Expand Down Expand Up @@ -50,30 +51,30 @@ def run(args):
# Setup output path for log file
# ---------------------------------------------------

fileHandler = logging.FileHandler(output_path + "/" + prefix + "graphbin2.log")
fileHandler = logging.FileHandler(f"{output_path}/{prefix}graphbin2.log")
fileHandler.setLevel(logging.DEBUG)
fileHandler.setFormatter(formatter)
logger.addHandler(fileHandler)

logger.info(
"Welcome to GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs using Assembly Graphs."
f"Welcome to GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs using Assembly Graphs."
)
logger.info(
"This version of GraphBin2 makes use of the assembly graph produced by metaFlye which is a long reads assembler based on the de Bruijn graph approach."
f"This version of GraphBin2 makes use of the assembly graph produced by metaFlye which is a long reads assembler based on the de Bruijn graph approach."
)

logger.info("Input arguments:")
logger.info("Contigs file: " + contigs_file)
logger.info("Assembly graph file: " + assembly_graph_file)
logger.info("Contig paths file: " + contig_paths)
logger.info("Abundance file: " + abundance_file)
logger.info("Existing binning output file: " + contig_bins_file)
logger.info("Final binning output file: " + output_path)
logger.info("Depth: " + str(depth))
logger.info("Threshold: " + str(threshold))
logger.info("Number of threads: " + str(nthreads))
logger.info(f"Input arguments:")
logger.info(f"Contigs file: {contigs_file}")
logger.info(f"Assembly graph file: {assembly_graph_file}")
logger.info(f"Contig paths file: {contig_paths}")
logger.info(f"Abundance file: {abundance_file}")
logger.info(f"Existing binning output file: {contig_bins_file}")
logger.info(f"Final binning output file: {output_path}")
logger.info(f"Depth: {depth}")
logger.info(f"Threshold: {threshold}")
logger.info(f"Number of threads: {nthreads}")

logger.info("GraphBin2 started")
logger.info(f"GraphBin2 started")

start_time = time.time()

Expand Down Expand Up @@ -231,9 +232,9 @@ def run(args):
except BaseException as err:
logger.error(f"Unexpected {err}")
logger.error(
"Please make sure that the correct path to the assembly graph file is provided."
f"Please make sure that the correct path to the assembly graph file is provided."
)
logger.info("Exiting GraphBin2... Bye...!")
logger.info(f"Exiting GraphBin2... Bye...!")
sys.exit(1)

logger.info(f"Total number of contigs available: {node_count}")
Expand All @@ -260,12 +261,12 @@ def run(args):
except BaseException as err:
logger.error(f"Unexpected {err}")
logger.error(
"Please make sure that the correct path to the assembly graph file is provided."
f"Please make sure that the correct path to the assembly graph file is provided."
)
logger.info("Exiting GraphBin2... Bye...!")
logger.info(f"Exiting GraphBin2... Bye...!")
sys.exit(1)

logger.info("Total number of edges in the assembly graph: " + str(len(edge_list)))
logger.info(f"Total number of edges in the assembly graph: {len(edge_list)}")

# Get the number of bins from the initial binning result
# --------------------------------------------------------
Expand All @@ -282,14 +283,14 @@ def run(args):
bins_list.sort()

n_bins = len(bins_list)
logger.info("Number of bins available in binning result: " + str(n_bins))
logger.info(f"Number of bins available in binning result: {n_bins}")

except BaseException as err:
logger.error(f"Unexpected {err}")
logger.error(
"Please make sure that the correct path to the binning result file is provided and it is having the correct format"
f"Please make sure that the correct path to the binning result file is provided and it is having the correct format"
)
logger.info("Exiting GraphBin2... Bye...!")
logger.info(f"Exiting GraphBin2... Bye...!")
sys.exit(1)

# Get initial binning result
Expand All @@ -312,9 +313,9 @@ def run(args):
except BaseException as err:
logger.error(f"Unexpected {err}")
logger.error(
"Please make sure that you have provided the correct assembler type and the correct path to the binning result file in the correct format."
f"Please make sure that you have provided the correct assembler type and the correct path to the binning result file in the correct format."
)
logger.info("Exiting GraphBin2... Bye...!")
logger.info(f"Exiting GraphBin2... Bye...!")
sys.exit(1)

# Get binned and unbinned contigs
Expand All @@ -334,8 +335,8 @@ def run(args):
binned_contigs.sort()
unbinned_contigs.sort()

logger.info("No. of binned contigs: " + str(len(binned_contigs)))
logger.info("No. of unbinned contigs: " + str(len(unbinned_contigs)))
logger.info(f"No. of binned contigs: {len(binned_contigs)}")
logger.info(f"No. of unbinned contigs: {len(unbinned_contigs)}")

# Get isolated vertices
# -----------------------------------------------------
Expand Down Expand Up @@ -397,12 +398,12 @@ def runBFS(node, threhold=depth):
# Remove labels of unsupported vertices
# -----------------------------------------------------

logger.info("Removing labels of unsupported vertices")
logger.info(f"Removing labels of unsupported vertices")

iter_num = 1

while True:
logger.debug("Iteration: " + str(iter_num))
logger.debug(f"Iteration: {iter_num}")

remove_labels = {}

Expand Down Expand Up @@ -476,14 +477,14 @@ def runBFS(node, threhold=depth):
# Refine labels of inconsistent vertices
# -----------------------------------------------------

logger.info("Refining labels of inconsistent vertices")
logger.info(f"Refining labels of inconsistent vertices")

iter_num = 1

once_moved = []

while True:
logger.debug("Iteration: " + str(iter_num))
logger.debug(f"Iteration: {iter_num}")

contigs_to_correct = {}

Expand Down Expand Up @@ -567,7 +568,7 @@ def runBFS(node, threhold=depth):

# Get non isolated contigs

logger.info("Obtaining non isolated contigs")
logger.info(f"Obtaining non isolated contigs")

# Initialise progress bar
pbar = tqdm(total=node_count)
Expand Down Expand Up @@ -614,18 +615,18 @@ def runBFS(node, threhold=depth):
# Close progress bar
pbar.close()

logger.info("Number of non-isolated contigs: " + str(len(non_isolated)))
logger.info(f"Number of non-isolated contigs: {len(non_isolated)}")

non_isolated_unbinned = list(set(non_isolated).intersection(set(unbinned_contigs)))

logger.info(
"Number of non-isolated unbinned contigs: " + str(len(non_isolated_unbinned))
f"Number of non-isolated unbinned contigs: {len(non_isolated_unbinned)}"
)

# Propagate labels to unlabelled vertices
# -----------------------------------------------------

logger.info("Propagating labels to unlabelled vertices")
logger.info(f"Propagating labels to unlabelled vertices")

# Initialise progress bar
pbar = tqdm(total=len(non_isolated_unbinned))
Expand Down Expand Up @@ -691,7 +692,7 @@ def __lt__(self, other):
# Determine contigs belonging to multiple bins
# -----------------------------------------------------

logger.info("Determining multi-binned contigs")
logger.info(f"Determining multi-binned contigs")

bin_cov_sum = [0 for x in range(n_bins)]
bin_contig_len_total = [0 for x in range(n_bins)]
Expand Down Expand Up @@ -763,9 +764,9 @@ def thread_function(
multi_bins = list(filter(lambda x: x is not None, mapped))

if len(multi_bins) == 0:
logger.info("No multi-labelled contigs were found")
logger.info(f"No multi-labelled contigs were found")
else:
logger.info("Found " + str(len(multi_bins)) + " multi-labelled contigs ==>")
logger.info(f"Found {len(multi_bins)} multi-labelled contigs ==>")

# Add contigs to multiplt bins
for contig, min_diff_combination in multi_bins:
Expand All @@ -782,7 +783,7 @@ def thread_function(
elapsed_time = time.time() - start_time

# Show elapsed time for the process
logger.info("Elapsed time: " + str(elapsed_time) + " seconds")
logger.info(f"Elapsed time: {elapsed_time} seconds")

# Sort contigs in bins
for i in range(n_bins):
Expand All @@ -791,7 +792,7 @@ def thread_function(
# Write result to output file
# -----------------------------------

logger.info("Writing the final binning results to file")
logger.info(f"Writing the final binning results to file")

output_bins = []

Expand Down Expand Up @@ -831,7 +832,7 @@ def thread_function(
line.append(bins_list[k])
output_bins.append(line)

output_file = output_path + prefix + "graphbin2_output.csv"
output_file = f"{output_path}{prefix}graphbin2_output.csv"

with open(output_file, mode="w") as output_file:
output_writer = csv.writer(
Expand All @@ -841,12 +842,12 @@ def thread_function(
for row in output_bins:
output_writer.writerow(row)

logger.info("Final binning results can be found at " + str(output_file.name))
logger.info(f"Final binning results can be found at {output_file.name}")

# Exit program
# -----------------------------------

logger.info("Thank you for using GraphBin2!")
logger.info(f"Thank you for using GraphBin2!")


def is_multi(
Expand Down
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