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Updated PhyloToL Part 1: GF assignment (markdown)

Godwin Ani 2024-08-12 15:16:50 -04:00
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PhyloToL-Part-1:-GF-assignment.md

@ -122,3 +122,13 @@ Role of each script
* **Main inputs** : A folder containing the [CDS](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/TestData), a folder containing the Databases, and a folder containing the [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/Scripts).
* **Outputs** : ReadyToGo files (AA and NTD) and taxon summary.
| Parameter | Type| Options| Description|
| ----------- | ----------------- |
| --first_script| int | 1, 2, 3, 4 | First script to run |
| --last_script | int | 2, 3, 4, 5 | First script to run|
| --cds| str|Path to a folder of nucleotide CDS| Each file name should start with a unique 10 digit code, and end in "_GenBankCDS.fasta", E.g. Op_me_hsap_GenBankCDS.fasta|
| --output| = str|Path for the output files | An "Output" folder will be created at this directory to contain all output files. By default this folder will be created at the parent directory of the Scripts folder |
| --genetic_code| str| Path to a file, Universal | If all of your taxa use the same genetic code, you may enter it here|
| --databases| str| Path to databases folder | The folder should contain all 3 databases|