86 lines
2.5 KiB
Python
Executable File
86 lines
2.5 KiB
Python
Executable File
#!/usr/bin/env python3
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"""
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Trinity FASTA Sequence Renaming Script
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Function: Rename sequences in FASTA file to format: [prefix@sequence_number]
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"""
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import sys
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import os
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def rename_fasta_sequences(input_file, prefix, output_file=None):
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"""
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Rename sequence headers in a FASTA file
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Parameters:
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input_file: Input FASTA filename
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prefix: Prefix for sequence names
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output_file: Output filename (optional, defaults to input_file_renamed.fasta)
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"""
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# Set output filename
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if output_file is None:
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file_base, file_ext = os.path.splitext(input_file)
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output_file = f"{file_base}_renamed{file_ext}"
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match_tsv = f"{output_file}.tsv"
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print(f"Input file: {input_file}")
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print(f"Output file: {output_file}")
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print(f"Naming format: {prefix}@mrna_<number>")
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print(f"Match TSV file: {match_tsv}")
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# Counter for sequences
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seq_count = 0
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try:
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with (
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open(input_file, "r") as fin,
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open(output_file, "w") as fout,
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open(match_tsv, "w") as tsvout,
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):
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tsvout.write("Original_Name\tNew_Name\n")
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for line in fin:
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if line.startswith(">"):
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# Sequence header line: rename it
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seq_count += 1
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original_name = line[1:].strip().split()[0]
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new_name = f"{prefix}@mrna_{seq_count}\n"
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fout.write(f">{new_name}")
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tsvout.write(f"{original_name}\t{new_name}\n")
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else:
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# Sequence data line: write as-is
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fout.write(line)
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print(f"Successfully renamed {seq_count} sequences")
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except FileNotFoundError:
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print(f"Error: Input file '{input_file}' not found")
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sys.exit(1)
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except Exception as e:
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print(f"Error processing file: {e}")
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sys.exit(1)
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def main():
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"""Main function"""
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if len(sys.argv) < 3:
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print("Usage: python script.py <fasta_file> <prefix> [output_file]")
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print("Example: python script.py sequences.fasta Gene new_sequences.fasta")
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sys.exit(1)
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input_file = sys.argv[1]
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prefix = sys.argv[2]
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output_file = sys.argv[3] if len(sys.argv) > 3 else None
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# Verify input file exists
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if not os.path.isfile(input_file):
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print(f"Error: File '{input_file}' does not exist")
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sys.exit(1)
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rename_fasta_sequences(input_file, prefix, output_file)
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if __name__ == "__main__":
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main()
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