YuuMJ1997/EukPhylo
1
0
Fork 0
mirror of http://43.156.76.180:8026/YuuMJ/EukPhylo.git synced 2025-12-28 20:50:25 +08:00
Code Issues Packages Projects Releases Wiki Activity

Updated PhyloToL Part 1: GF assignment (markdown)

Godwin Ani 2024-08-12 16:14:23 -04:00
parent a766fee515
commit d0859d044c
1 changed files with 8 additions and 22 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

30
PhyloToL-Part-1:-GF-assignment.md

@ -92,7 +92,7 @@ Available parameters are:
| --maxlen |int|-| Maximum transcript length |
| --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`
@ -100,8 +100,13 @@ To run the PhyloToL part 1 for both processing transcriptomes and removing seque
### Processing genomes
Role of each script
<img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/PTL1_Processing_Genomes_scripts.png" width="100%">
* **Main inputs** : A folder containing the [CDS](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/TestData), a folder containing the Databases, and a folder containing the [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/Scripts).
* **Outputs** : ReadyToGo files (AA and NTD) and taxon summary.
* **Main inputs** : The main inputs for processing genomes are: a folder containing the assembled [CDS](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/TestData), 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/Genomes/Scripts).
* **Outputs** : The main outputs after processing genomes 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 genomes, run:
`python Scripts/wrapper.py --first_script 1 --last_script 5 --cds CDS --output . --genetic_code Gcode.txt --databases Databases > log.txt`
| Parameter | Type| Options| Description|
@ -115,22 +120,3 @@ Role of each script
* *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.
* _Example:_
| Taxa | Genetic code |
| ----------- | --------- |
| EE_uc_Me03 | Universal |
| Sr_ci_Arsp | Ciliate |
| Sr_ci_Cpol | Peritrich |
| Sr_ci_Bjap | Blepharisma |
* *The Conspecific.txt is similar and is only needed for cross plate contamination removal.
* _Example:_
| Taxa | plate|
| ----------- | ----------------- |
| EE_uc_Me03 | Metatranscriptome |
| EE_uc_Me04 | Metatranscriptome |
| EE_uc_Me05 | Metatranscriptome |