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Updated QuickStart EukPhylo (markdown)

Godwin Ani 2025-01-28 14:20:35 -05:00
parent 7be7c99cbc
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QuickStart-EukPhylo.md

@ -63,7 +63,6 @@ Code parameters:
### Output: ### Output:
1. **ReadyToGo files = AA, NTD** 1. **ReadyToGo files = AA, NTD**
2. **Summary and statistics of sequences** 2. **Summary and statistics of sequences**
### Modularity of options and replacing the Hook database ### Modularity of options and replacing the Hook database
@ -87,19 +86,20 @@ To add the XPC option, only available for transcriptomes, user need to add the -
``` ```
python wrapper.py -1 1 -2 5 --cds CDS -o Output_Folder --genetic_code Gcodes.txt -d Databases > log.txt python wrapper.py -1 1 -2 5 --cds CDS -o Output_Folder --genetic_code Gcodes.txt -d Databases > log.txt
``` ```
Code flags: Code parameters:
* -1 = start/first script to run. | Parameter | Description|
* -2 = end/last script to run. | :--- |:--- |
* --cds = path to folder with CDS files in fasta format. | -1 | Start/first script to run.|
* -o = path to output folder | -2 | End/last script to run.|
* --genetic_code = specified genetic code, name of .txt file with Genetic codes; optional |--cds | Path to folder with CDS files in fasta format.|
* -d = path to Databases folder |-o | Path to output folder.|
* log.txt = if added to the end of the command, it will output a log file with progress, warning, or error messages |--genetic_code | Specified genetic code, name of .txt file with Genetic codes; optional.|
|-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.|
### Output: ### Output:
> ReadyToGo files = AA, NTD 1. **ReadyToGo files = AA, NTD**
2. **Summary and statistics of sequences**
> Summary and statistics of sequences
### Modularity of options and replacing the Hook database ### Modularity of options and replacing the Hook database
EukPhylo part 1 for genomes is composed of 5 scripts. User can choose to start or stop at each step by changing the -1 and/or -2 options. EukPhylo part 1 for genomes is composed of 5 scripts. User can choose to start or stop at each step by changing the -1 and/or -2 options.