From d8654eadec08416dae2a73bbbbec2163b0a9e796 Mon Sep 17 00:00:00 2001 From: GiuliaRibeiro <41350697+GiuliaRibeiro@users.noreply.github.com> Date: Thu, 10 Apr 2025 09:15:47 -0400 Subject: [PATCH] Updated EukPhylo QuickStart (markdown) --- EukPhylo-QuickStart.md | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/EukPhylo-QuickStart.md b/EukPhylo-QuickStart.md index c666f15..bd78935 100644 --- a/EukPhylo-QuickStart.md +++ b/EukPhylo-QuickStart.md @@ -131,14 +131,7 @@ If a user choose to use their own gene families database, they need to replace t In a main project directory: * Create a `Scripts` folder containing the 8 scripts from GitHub [here](https://github.com/Katzlab/EukPhylo/tree/main/PTL2/Scripts) * In addition to the scripts, also add the `trimal-trimAl` and `guidance.v2.02` folders, as downloaded from [here](https://github.com/inab/trimal) and [here](https://github.com/anzaika/guidance). Smith College HPC (Grid) users see [here](https://docs.google.com/document/d/1tDxaCrVEHckyvlaaY58lNQnJ4UHTRAMICdR7xzzjPTE/edit?tab=t.0) - * IMPORTANT NOTE: Please make sure to correct the paths in the `guidance.py` script with the full path of the location of your `trimal-trimAl` and `guidance.v2.02`. - Lines to modify: - `os.system('python [full path for guidance]/guidance.pl --seqFile ' + guidance_input + '/' + file + ' --msaProgram MAFFT --seqType aa --outDir ' + tax_guidance_outdir + ' --seqCutoff ' + str(params.seq_cutoff) + ' --colCutoff ' + str(params.col_cutoff) + " --outOrder as_input --bootstraps 10 --MSA_Param '\\--" + mafft_alg + " --maxiterate 1000 --thread " + str(params.guidance_threads) + " --bl 62 --anysymbol' > " + params.output + '/Output/Intermediate/Guidance/Output/' + file[:10] + '/log.txt') -` - and here: - `#Gap trimming - os.system('Scripts/trimal-trimAl/source/trimal -in ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.postGuidance_preTrimAl_aligned.fasta -out ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.95gapTrimmed.fasta -gapthreshold ' + str(params.trimal_cutoff) + ' -fasta') -` + * IMPORTANT NOTE: Please make sure to correct the paths in the `guidance.py` script with the full path of the location of your `trimal-trimAl` and `guidance.v2.02` as exemplified in the script. * Create an empty output folder (e.g. `Output`) for results (i.e. guidance and tree outputs) * Create a list of ten-digit codes for your target and outgroup taxa (e.g. `taxa.txt`) * Create a folder (e.g. `R2Gs`) that contains the AA ReadyToGo fasta files for all taxa (from `taxa.txt`)