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In the Prodigal GFF file, the metadata ID field is a generated unique ID that is in the format 1_1, 1_2, 2_1, 2_2, etc. This is a problem if people concatenate all the GFFs together since then the unique IDs aren't unique. In DRAM1, the IDs were repalced with the SeqID_Genenumber. So that is what we are doing here We also replaced the python script that parsed the GFF into a summary TSV for later use in DRAM2 into a tsv and replaced with with bash parsing. Which benchmarking showed to be around 10-50 times faster.
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Pull Request Overview
This PR renames ID columns in Prodigal GFF files to ensure uniqueness when multiple files are concatenated, and replaces a Python script with faster bash parsing for GFF to TSV conversion.
- Replace generated IDs (1_1, 1_2, etc.) with SeqID_GeneNumber format for uniqueness
- Switch from Python script to bash parsing for GFF to TSV conversion (10-50x faster)
- Add ID replacement functionality using new bash script
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In the Prodigal GFF file, the metadata ID field is a generated unique ID that is in the format 1_1, 1_2, 2_1, 2_2, etc. This is a problem if people concatenate all the GFFs together since then the unique IDs aren't unique. In DRAM1, the IDs were repalced with the SeqID_Genenumber. So that is what we are doing here
We also replaced the python script that parsed the GFF into a summary TSV for later use in DRAM2 into a tsv and replaced with with bash parsing. Which benchmarking showed to be around 10-50 times faster.