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Updated PhyloToL Part 1: GF assignment (markdown)

Godwin Ani 2024-08-12 15:49:58 -04:00
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PhyloToL-Part-1:-GF-assignment.md

@ -71,6 +71,47 @@ Replacing the PhyloToL Hook DB with a user-defined set of gene families is strai
Role of each script
<img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/PTL1_Processing_Transcriptomes_scripts.png" width="100%">
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`
Available parameters are:
| Parameter | Type| Options| Description|
| ----------- | ----------------- |----------- | ----------------- |
| --first_script |int |1, 2, 3, 4, 5, 6 | First script to run |
| --last_script |int|1, 2, 3, 4, 5, 6, 7 | Last script to run |
| --assembled_transcripts |str|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 |
| --databases| str| Path to databases folder | The folder should contain all 3 databases|
| --output|str|Path for the output files | 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 |
|--xplate_contam |-|- | Run cross-plate contamination removal (includes all files) |
| --genetic_code |str|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| If all of your taxa use the same genetic code, you may enter it here. 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 file. |
|--conspecific_names |str| 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. |
| --minlen |int| -| Minimum transcript length |
| --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:
`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
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.
| Parameter | Type| Options| Description|
| ----------- | ----------------- |----------- | ----------------- |
| --first_script| int | 1, 2, 3, 4 | First script to run |
| --last_script | int | 2, 3, 4, 5 | First script to run|
| --cds| str|Path to a folder of nucleotide CDS| Each file name should start with a unique 10 digit code, and end in "_GenBankCDS.fasta", E.g. Op_me_hsap_GenBankCDS.fasta|
| --output|str|Path for the output files | 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 |
| --genetic_code| str| Path to a file, Universal | If all of your taxa use the same genetic code, you may enter it here|
| --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
@ -91,44 +132,4 @@ Role of each script
| ----------- | ----------------- |
| EE_uc_Me03 | Metatranscriptome |
| EE_uc_Me04 | Metatranscriptome |
| EE_uc_Me05 | Metatranscriptome |
To process transcriptomes, run:
`python Scripts/wrapper.py -1 1 -2 7 --assembled_transcripts AssembledTranscripts --output . --genetic_code Universal -d Databases > log.txt`
| Parameter | Type| Options| Description|
| ----------- | ----------------- |----------- | ----------------- |
| --first_script |int |1, 2, 3, 4, 5, 6 | First script to run |
| --last_script |int|1, 2, 3, 4, 5, 6, 7 | Last script to run |
| --assembled_transcripts |str|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 |
| --databases| str| Path to databases folder | The folder should contain all 3 databases|
| --output|str|Path for the output files | 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 |
|--xplate_contam |str|x | Run cross-plate contamination removal (includes all files) |
| --genetic_code |str|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| If all of your taxa use the same genetic code, you may enter it here. 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 file. |
|--conspecific_names |str| 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. |
| --minlen |int| -| Minimum transcript length |
| --maxlen |int|-| Maximum transcript length |
| --seq_count |int|-| 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
* *For running with cross plate contamination removal, add `-x -n Conspecific.txt` to the line of code.
### 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.
| Parameter | Type| Options| Description|
| ----------- | ----------------- |----------- | ----------------- |
| --first_script| int | 1, 2, 3, 4 | First script to run |
| --last_script | int | 2, 3, 4, 5 | First script to run|
| --cds| str|Path to a folder of nucleotide CDS| Each file name should start with a unique 10 digit code, and end in "_GenBankCDS.fasta", E.g. Op_me_hsap_GenBankCDS.fasta|
| --output|str|Path for the output files | 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 |
| --genetic_code| str| Path to a file, Universal | If all of your taxa use the same genetic code, you may enter it here|
| --databases| str| Path to databases folder | The folder should contain all 3 databases|
| EE_uc_Me05 | Metatranscriptome |