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Updated PhyloToL Part 1: GF assignment (markdown)

Godwin Ani 2024-08-12 13:06:01 -04:00
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PhyloToL-Part-1:-GF-assignment.md

@ -95,7 +95,14 @@ Role of each script
To process transcriptomes, run:
`python wrapper.py -1 1 -2 7 --assembled_transcripts AssembledTranscripts -o . --genetic_code Universal -d Databases > log.txt`
`python Scripts/wrapper.py -1 1 -2 7 --assembled_transcripts AssembledTranscripts --output . --genetic_code Universal -d Databases > log.txt`
* -1 = start script
* -2 = end script
* --assembled_transcripts = Folder with Assembled transcripts in fasta format
* --output = path to output folder
* --genetic_code = specified genetic code, name of .txt file with Genetic codes
* -d = path to Databases folder
* > log.txt = if added to the end of the command, it will output a log file with progress, warning, or error messages
### Processing genomes