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Updated PhyloToL Part 1: GF assignment (markdown)

Godwin Ani 2024-08-12 15:00:14 -04:00
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PhyloToL-Part-1:-GF-assignment.md

@ -96,12 +96,23 @@ Role of each script
To process transcriptomes, run: To process transcriptomes, run:
`python Scripts/wrapper.py -1 1 -2 7 --assembled_transcripts AssembledTranscripts --output . --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 | Parameter | Description|
* --assembled_transcripts = Folder with Assembled transcripts in fasta format | ----------- | ----------------- |
* --output = path to output folder | -1, --first_script | First script to run |
* --genetic_code = specified genetic code, name of .txt file with Genetic codes | -2, --last_script | Last script to run |
* -d = path to Databases folder | -a, --assembled_transcripts | Path to a folder of assembled transcripts, assembled by rnaSPAdes. Each assembled transcript file name should start with a unique 10 digit code, and end in "_assembledTranscripts.fasta", E.g. Op_me_hsap_assembledTranscripts.fasta |
| -d, --databases | Path to databases folder |
| -o, --output | 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 |
| -x, --xplate_contam | Run cross-plate contamination removal (includes all files) |
| -g, --genetic_code | If all of your taxa use the same genetic code, you may enter it here (to be used in script 5). Alternatively, if you need to use a variety of genetic codes but know which codes to use, you may fill give here the path to a .txt or .tsv with two tab-separated columns, the first with the ten-digit codes and the second column with the corresponding genetics codes |
| -n, --conspecific_names | A .txt or .tsv file with two tab-separated columns; the first should have 10 digit codes, the second species or other identifying names. This is used to determine which sequences to remove (only between "species") in cross-plate contamination assessment. |
| -min, --minlen | Minimum transcript length |
| -max, --maxlen | Maximum transcript length |
| -c, --seq_count | minimum number of sequences after assigning OGs |
* \>log.txt = if added to the end of the command, it will output a log file with progress, warning, or error messages * \>log.txt = if added to the end of the command, it will output a log file with progress, warning, or error messages
* *For running with cross plate contamination removal, add `-x -n Conspecific.txt` to the line of code. * *For running with cross plate contamination removal, add `-x -n Conspecific.txt` to the line of code.