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Updated PhyloToL Part 1: GF assignment (markdown)

Godwin Ani 2024-08-12 16:02:22 -04:00
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PhyloToL-Part-1:-GF-assignment.md

@ -74,7 +74,7 @@ Role of each script
* **Main inputs** : The main inputs for processing transcriptomes are: a folder containing the assembled [transcripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/TestData) (as described above), a folder containing the Databases with three subfolders(db_BvsE (how we ID likely-bacterial sequences), db_StopFreq (for stop codon assignment), and db_OG (this must be current version of the hook)), and a folder containing the [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/Scripts). * **Main inputs** : The main inputs for processing transcriptomes are: a folder containing the assembled [transcripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/TestData) (as described above), a folder containing the Databases with three subfolders(db_BvsE (how we ID likely-bacterial sequences), db_StopFreq (for stop codon assignment), and db_OG (this must be current version of the hook)), and a folder containing the [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/Scripts).
* **Outputs** : The main outputs after processing transcriptomes are: ReadyToGo files which contain the nucleotide and amino acid sequences of each taxa, and a summary information of the sequences processed for each taxa. * **Outputs** : The main outputs after processing transcriptomes are: ReadyToGo files which contain the nucleotide and amino acid sequences of each taxa, and a summary information of the sequences processed for each taxa.
####To run the PhyloToL part 1 for processing transcriptomes, run: ###To run the PhyloToL part 1 for processing transcriptomes, run:
`python Scripts/wrapper.py --first_script 1 --last_script 7 --assembled_transcripts AssembledTranscripts --output . --genetic_code Gcode.txt --databases Databases > log.txt` `python Scripts/wrapper.py --first_script 1 --last_script 7 --assembled_transcripts AssembledTranscripts --output . --genetic_code Gcode.txt --databases Databases > log.txt`
Available parameters are: Available parameters are: