Mercurial > repos > abims-sbr > filter_assemblies
changeset 3:faadbce1bbd2 draft default tip
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ee0948efcef5f8732f7f32ce37a8127d891d0c64
| author | abims-sbr |
|---|---|
| date | Thu, 11 Sep 2025 08:27:22 +0000 |
| parents | 000dbfafe31d |
| children | |
| files | filter_assembly.xml scripts/S01_script_to_choose.py |
| diffstat | 2 files changed, 5 insertions(+), 1 deletions(-) [+] |
line wrap: on
line diff
--- a/filter_assembly.xml Mon Jun 30 12:23:02 2025 +0000 +++ b/filter_assembly.xml Thu Sep 11 08:27:22 2025 +0000 @@ -1,4 +1,4 @@ -<tool name="Filter assemblies" id="filter_assemblies" version="2.0.5"> +<tool name="Filter assemblies" id="filter_assemblies" version="2.0.6"> <description> Filter the outputs of Spades, Velvet or Trinity assemblies
--- a/scripts/S01_script_to_choose.py Mon Jun 30 12:23:02 2025 +0000 +++ b/scripts/S01_script_to_choose.py Thu Sep 11 08:27:22 2025 +0000 @@ -5,6 +5,7 @@ from Bio import SeqIO + def fasta_formatter(input_file, output_file): """ Reformats the input FASTA file to ensure that sequences @@ -26,6 +27,7 @@ if sequence: outfile.write(sequence + '\n') + def reformat_headers(input_file, output_file, prefix): """ Reformats the headers of the FASTA records by adding a specified prefix @@ -76,6 +78,7 @@ # Write output file with new headers SeqIO.write(modified_sequences, output_fasta, "fasta") + def main(): if len(sys.argv) < 5: print( @@ -156,5 +159,6 @@ os.remove(cap_contigs_file) os.remove(name_fasta_final) + if __name__ == "__main__": main()