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Updated PhyloToL Part 1: GF assignment (markdown)

Godwin Ani 2024-08-12 16:02:07 -04:00
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PhyloToL-Part-1:-GF-assignment.md

@ -71,9 +71,11 @@ Replacing the PhyloToL Hook DB with a user-defined set of gene families is strai
Role of each script Role of each script
<img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/PTL1_Processing_Transcriptomes_scripts.png" width="100%"> <img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/PTL1_Processing_Transcriptomes_scripts.png" width="100%">
* **Main inputs** : The main inputs for processing transcriptomes are: a folder containing the assembled [transcripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/TestData) (as described above), a folder containing the Databases with three subfolders(db_BvsE (how we ID likely-bacterial sequences), db_StopFreq (for stop codon assignment), and db_OG (this must be current version of the hook)), and a folder containing the [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/Scripts).
* **Outputs** : The main outputs after processing transcriptomes are: ReadyToGo files which contain the nucleotide and amino acid sequences of each taxa, and a summary information of the sequences processed for each taxa.
To run the PhyloToL part 1 for processing transcriptomes, run: ####To run the PhyloToL part 1 for processing transcriptomes, run:
* `python Scripts/wrapper.py --first_script 1 --last_script 7 --assembled_transcripts AssembledTranscripts --output . --genetic_code Gcode.txt --databases Databases > log.txt` `python Scripts/wrapper.py --first_script 1 --last_script 7 --assembled_transcripts AssembledTranscripts --output . --genetic_code Gcode.txt --databases Databases > log.txt`
Available parameters are: Available parameters are:
| Parameter | Type| Options| Description| | Parameter | Type| Options| Description|
@ -90,11 +92,11 @@ Available parameters are:
| --maxlen |int|-| Maximum transcript length | | --maxlen |int|-| Maximum transcript length |
| --seq_count |int|-| minimum number of sequences after assigning OGs | | --seq_count |int|-| minimum number of sequences after assigning OGs |
To run the PhyloToL part 1 for both processing transcriptomes and removing sequences that resulted from index switching (cross plate contamination), run: To run the PhyloToL part 1 for both processing transcriptomes and removing sequences that resulted from index switching (cross plate contamination), run:
`python Scripts/wrapper.py --first_script 1 --last_script 7 --assembled_transcripts AssembledTranscripts --output . --genetic_code Gcode.txt --databases Databases --xplate_contam --conspecific_names Conspecific.txt > log.txt` `python Scripts/wrapper.py --first_script 1 --last_script 7 --assembled_transcripts AssembledTranscripts --output . --genetic_code Gcode.txt --databases Databases --xplate_contam --conspecific_names Conspecific.txt > log.txt`
### Processing genomes ### Processing genomes
Role of each script Role of each script
<img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/PTL1_Processing_Genomes_scripts.png" width="100%"> <img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/PTL1_Processing_Genomes_scripts.png" width="100%">
@ -112,8 +114,7 @@ Role of each script
| --databases| str| Path to databases folder | The folder should contain all 3 databases| | --databases| str| Path to databases folder | The folder should contain all 3 databases|
* **Main inputs** : A folder containing the assembled [transcripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/TestData), a folder containing the Databases, and a folder containing the [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/Scripts).
* **Outputs** : ReadyToGo files (AA and NTD) and taxon summary.
* *Optional inputs : Gcodes.txt and Conspecific.txt * *Optional inputs : Gcodes.txt and Conspecific.txt
* *The Gcodes.txt is a tab separated txt file containing the genetic code of the taxa. This will most likely not be needed except for some organisms like ciliates. * *The Gcodes.txt is a tab separated txt file containing the genetic code of the taxa. This will most likely not be needed except for some organisms like ciliates.
* _Example:_ * _Example:_