NadineWolgast
commented
1 week ago Dear Luke,
FusionCatcher does not natively support output in BEDPE format. However, you can convert the final-list_candidate-fusion-genes.txt file into BEDPE format using a Python script. Below is a method to achieve this:
Script: convert_to_bedpe.py
This script reads the final-list_candidate-fusion-genes.txt file produced by FusionCatcher and converts it into BEDPE format. It extracts key columns such as chromosome, start/end positions, strand, and fusion gene names to construct the BEDPE file.
#!/usr/bin/env python3
import csv
import sys
def convert_to_bedpe(input_file, output_file):
"""
Converts FusionCatcher's output into BEDPE format.
:param input_file: Path to FusionCatcher's `final-list_candidate-fusion-genes.txt`.
:param output_file: Path to the output BEDPE file.
"""
with open(input_file, 'r') as infile, open(output_file, 'w') as outfile:
reader = csv.reader(infile, delimiter='\t')
writer = csv.writer(outfile, delimiter='\t')
# Write BEDPE header
writer.writerow(["chrom1", "start1", "end1", "chrom2", "start2", "end2", "name", "score", "strand1", "strand2"])
# Skip header line of FusionCatcher file
header = next(reader)
for line in reader:
# Skip invalid rows
if len(line) < 10:
print(f"Skipping invalid row: {line}")
continue
try:
# Extract relevant data
gene1 = line[0]
gene2 = line[1]
chrom1, pos1_str, strand1 = line[8].split(':') # Fusion_point_for_gene_1
chrom2, pos2_str, strand2 = line[9].split(':') # Fusion_point_for_gene_2
pos1 = int(pos1_str)
pos2 = int(pos2_str)
# Define BEDPE fields
start1 = pos1 - 1
end1 = pos1
start2 = pos2 - 1
end2 = pos2
fusion_name = f"{gene1}-{gene2}"
score = 0 # Placeholder for score
# Write the BEDPE line
writer.writerow([chrom1, start1, end1, chrom2, start2, end2, fusion_name, score, strand1, strand2])
except ValueError as e:
print(f"Skipping row due to error: {e}")
continue
# Main execution
if __name__ == "__main__":
if len(sys.argv) != 3:
print("Usage: python3 convert_to_bedpe.py <input_file> <output_file>")
sys.exit(1)
input_file = sys.argv[1]
output_file = sys.argv[2]
convert_to_bedpe(input_file, output_file)
print(f"Conversion complete. BEDPE file saved to {output_file}")Best, Nadine
SysLuke
Dear ndaniel,
I am using FusionCatcher for gene fusion prediction and would like to output the predicted results in BEDPE format. Is there any existing command-line option or configuration to directly convert FusionCatcher's output into BEDPE format?
If FusionCatcher does not provide this feature, could you suggest any methods to convert the final-list_candidate-fusion-genes.txt file into BEDPE format?
Thank you for any advice or solutions you can provide.
Best regards, Luke