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Updated PhyloToL Part 1: GF assignment (markdown)

Godwin Ani 2024-08-12 15:25:28 -04:00
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PhyloToL-Part-1:-GF-assignment.md

@ -97,19 +97,19 @@ To process transcriptomes, run:
`python Scripts/wrapper.py -1 1 -2 7 --assembled_transcripts AssembledTranscripts --output . --genetic_code Universal -d Databases > log.txt`
| Parameter | Description|
| ----------- | ----------------- |
| -1, --first_script | First script to run |
| -2, --last_script | Last script to run |
| -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 |
| 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 |
@ -128,7 +128,7 @@ Role of each script
| --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 |
| --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|