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Update ProcessAndRenameAssembledData.py

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Adri K. Grow 2025-06-27 12:39:05 -04:00 committed by GitHub
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Utilities/For_Assemblies/ProcessAndRenameAssembledData.py
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''' '''
Author & Date: Adri K. Grow + ChatGPT, Nov 11th 2024 Author & Date: Adri K. Grow + ChatGPT, Nov 11th 2024
- Updated 02/13/25 to accept either transcriptome and genome assembled data in command line - Updated 02/13/25 to accept either transcriptome and genome assembled data in command line
Motivation: assess and rename assembled transcript or genome files for PTL6p1 (or EPv1p1) 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 assembled file, named 'WTA_LKH<xxxx>' or 'WGA_LKH<xxxx>', each containing a 'transcripts.fasta' or 'contigs.fasta' file