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Update ProcessAndRenameAssembledData.py

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Adri K. Grow 2025-08-21 10:40:08 -04:00 committed by GitHub
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Utilities/For_Assemblies/ProcessAndRenameAssembledData.py
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@ -4,7 +4,7 @@ Author & Date: Adri K. Grow + ChatGPT, Nov 11th 2024
Motivation: assess and rename assembled transcript or genome files for use in EukPhylo Part 1 Motivation: assess and rename assembled transcript or genome files for use in EukPhylo Part 1
Intention: warn if any 'transcripts.fasta' or 'contigs.fasta' files are missing or empty for an LKH, otherwise rename and copy them with their assigned 10-digit code by LKH Intention: warn if any 'transcripts.fasta' or 'contigs.fasta' files are missing or empty for an LKH, otherwise rename and copy them with their assigned 10-digit code by LKH
Input: Input:
- a base directory containing subdirectories for each LKH assembled file, named 'WTA_LKH<xxxx>' or 'WGA_LKH<xxxx>', each containing a 'transcripts.fasta' or 'contigs.fasta' file - a base directory containing subdirectories for each LKH, named either 'WTA_LKH<xxxx>' or 'WGA_LKH<xxxx>', each containing a 'transcripts.fasta' or 'contigs.fasta' file
- a mapping .txt file with LKH#s tab-separated with corresponding 10-digit codes - a mapping .txt file with LKH#s tab-separated with corresponding 10-digit codes
Output: Output:
- a folder named 'renamed_transcripts|contigs' with assembled files now named by 10-digit codes; e.g. "Sr_rh_Ro04_assembledTranscripts.fasta" - a folder named 'renamed_transcripts|contigs' with assembled files now named by 10-digit codes; e.g. "Sr_rh_Ro04_assembledTranscripts.fasta"
@ -83,3 +83,4 @@ def main():
if __name__ == "__main__": if __name__ == "__main__":
main() main()