From ca55d509c58a2e5211beb3f5f69fb0fbe08e3e37 Mon Sep 17 00:00:00 2001 From: Godwin Ani Date: Mon, 12 Aug 2024 13:06:01 -0400 Subject: [PATCH] Updated PhyloToL Part 1: GF assignment (markdown) --- PhyloToL-Part-1:-GF-assignment.md | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/PhyloToL-Part-1:-GF-assignment.md b/PhyloToL-Part-1:-GF-assignment.md index beadc76..96599ed 100644 --- a/PhyloToL-Part-1:-GF-assignment.md +++ b/PhyloToL-Part-1:-GF-assignment.md @@ -95,7 +95,14 @@ Role of each script To process transcriptomes, run: -`python wrapper.py -1 1 -2 7 --assembled_transcripts AssembledTranscripts -o . --genetic_code Universal -d Databases > log.txt` +`python Scripts/wrapper.py -1 1 -2 7 --assembled_transcripts AssembledTranscripts --output . --genetic_code Universal -d Databases > log.txt` +* -1 = start script +* -2 = end script +* --assembled_transcripts = Folder with Assembled transcripts in fasta format +* --output = path to output folder +* --genetic_code = specified genetic code, name of .txt file with Genetic codes +* -d = path to Databases folder +* > log.txt = if added to the end of the command, it will output a log file with progress, warning, or error messages ### Processing genomes