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Updated PhyloToL Part 1: GF assignment (markdown)

Katzlab 2024-10-15 16:19:14 +01:00
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PhyloToL-Part-1:-GF-assignment.md

@ -89,7 +89,8 @@ PhyloToL part 1 starts with your **assembled transcripts** and produces **ReadyT
On a grid
`python Scripts/wrapper.py --first_script 1 --last_script 7 --assembled_transcripts AssembledTranscripts --genetic_code Gcode.txt --databases Databases > log.txt`
On a local computer: navigate to within the Scripts folder
On a local computer: First navigate to within the Scripts folder and then run:
`python3 wrapper.py --first_script 1 --last_script 7 --assembled_transcripts [full_path]/PhyloToL-6/PTL1/Transcriptomes/AssembledTranscripts --genetic_code universal --databases [full_path]/PhyloToL-6/PTL1/Transcriptomes/Databases --output [full_path]/PhyloToL-6/PTL1/Transcriptomes/ > log.txt`
In this case, the file `Gcode.txt` is a text file designating genetic code assignments for each taxon. The file should contain two tab-separated columns; the first column gives a ten-digit sample identifier, and the second column the genetic code assignment to be used in translation (script 5). The genetic code options are: universal, blepharisma, chilodonella, condylostoma, euplotes, peritrich, vorticella, ciliate, mesodinium, taa, tag, tga, and none. If you are not working with ciliates, you should probably choose "universal" for each taxon, or just use the argument `--genetic_code universal` instead of creating a text file.