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Updated PhyloToL Part 1: GF assignment (markdown)

Godwin Ani 2024-08-13 10:47:51 -04:00
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PhyloToL-Part-1:-GF-assignment.md

@ -71,7 +71,7 @@ Replacing the PhyloToL Hook DB with a user-defined set of gene families is strai
Role of each script
<img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/PTL1_Processing_Transcriptomes_scripts.png" width="100%">
Running PhyloToL Part 1 on transcriptomes requires at least 3 items in your main directory: 1) A folder named Scripts and containing all [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/Scripts) from PhyloToL part 1 github, 2) a folder containing your assembled [transcripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/TestData) (as described above), and 3) 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 (The hook database as described above)). Default script starts with assembled transcripts and produces ReadyToGo files (nucleotide and amino acid sequences) of each taxa, and a summary information of the sequences processed for those taxa.
Running PhyloToL Part 1 on transcriptomes requires at least 3 items in your main directory: 1) A folder named Scripts and containing all [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/Scripts) from PhyloToL part 1 github, 2) a folder containing your assembled [transcripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/TestData) (as described above), and 3) 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 (The hook database as described above)). Default script starts with your assembled transcripts and produces ReadyToGo files (nucleotide and amino acid sequences) of each taxa, and a summary information of the sequences processed for those taxa.
* 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`
@ -110,7 +110,7 @@ Example of a Conspecific.txt file
Role of each script
<img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/PTL1_Processing_Genomes_scripts.png" width="100%">
Running PhyloToL Part 1 on genomes requires at least 3 items in your main directory: 1) A folder named Scripts and containing all [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/Scripts) from PhyloToL part 1 github, 2) a folder containing your assembled [CDS](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/TestData) (as described above), and 3) 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 (The hook database as described above)). Default script starts with assembled transcripts and produces ReadyToGo files (nucleotide and amino acid sequences) of each taxa, and a summary information of the sequences processed for those taxa.
Running PhyloToL Part 1 on genomes requires at least 3 items in your main directory: 1) A folder named **Scripts** and containing all [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/Scripts) from PhyloToL part 1 github, 2) a folder containing your **[CDS](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/TestData)** (as described above), and 3) 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 (The hook database as described above)). Default script starts with your **CDS** and produces **ReadyToGo files** (nucleotide and amino acid sequences) of each taxa, and **summary information** of the sequences processed for those taxa.
#### To run the PhyloToL part 1 for processing genomes, run: