From 4b1197eaee73020d620ede90bd146f04a68494bb Mon Sep 17 00:00:00 2001 From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com> Date: Sat, 20 Jan 2024 13:58:41 -0500 Subject: [PATCH] Headers in 4_InFrameStopCodonEstimator.py --- .../Scripts/4_InFrameStopCodonEstimator.py | 86 ++++++++----------- 1 file changed, 37 insertions(+), 49 deletions(-) diff --git a/PTL1/Transcriptomes/Scripts/4_InFrameStopCodonEstimator.py b/PTL1/Transcriptomes/Scripts/4_InFrameStopCodonEstimator.py index d707dd0..ae21d52 100644 --- a/PTL1/Transcriptomes/Scripts/4_InFrameStopCodonEstimator.py +++ b/PTL1/Transcriptomes/Scripts/4_InFrameStopCodonEstimator.py @@ -9,6 +9,43 @@ # if unsure. This step can be skipped if genetic codes were input from the beginning. This # script should be run through the PhyloToL 6 Part 1 pipeline using the script wrapper.py. +#----------------------------------------- NOTES -----------------------------------------# +# +# This script is designed to HELP you make an informed decision about the genetic code being +# used by your particular organism. Be aware that it will be limited by the quality of the +# data given to it! +# +# You will need: +# +# Diamond, BioPython, AND the output from '3_AssignOGs.py' +# +#------------------------------- Interpretation of Results -------------------------------# +# +# Example output using CILIATE (TGA) genetic Code (NOTE THE In-Frame Densities): +# +# Stop Codon Number_of_Seqs_Analyzed In-frame TAG In-frame TGA In-frame TAA Total Codons In-frame TAG density In-frame TGA density In-frame TAA density +# TGA 341 14 0 22 113156 1.2 0 0.92 +# TAG 424 0 0 34 140085 0 0 0.78 +# TAA 205 14 0 0 16714 0.84 0 0 +# Summary 970 28 0 56 269955 2.04 0 1.7 +# +# VALUES in summary line (OR SUM of Density) that are > 1.5 likely indicate that the STOP +# codon has been reassigned... in the case above, TAG and TAA look like they have been +# reassigned. +# +# +# Example output using UNIVERSAL genetic Code (NOTE THE In-Frame Densities): +# +# Stop Codon Number_of_Seqs_Analyzed In-frame TAG In-frame TGA In-frame TAA Total Codons In-frame TAG density In-frame TGA density In-frame TAA density +# TGA 341 1 0 2 113156 0.2 0 0.05 +# TAG 424 0 2 4 140085 0 0 0.08 +# TAA 205 1 0 0 16714 0.04 0 0 +# Summary 970 2 2 6 269955 0.15 0 0.06 +# +# VALUES in summary line (OR SUM of Density) that are > 0.5 likely indicate that the STOP +# codon still acts as STOP... in the case above, TAG, TGA and TAA look like they still behave +# as a stop codon. + import argparse, os, sys from argparse import RawTextHelpFormatter,SUPPRESS from distutils import spawn @@ -720,52 +757,3 @@ def main(): next_script(args) main() - - -#----------------------------------------- NOTES -----------------------------------------# -# -# This script is designed to HELP you make an informed decision about the genetic code being -# used by your particular organism. Be aware that it will be limited by the quality of the -# data given to it! -# -# You will need: -# -# Diamond, BioPython, AND the output from '3_CountOGSDiamond.py' -# -# If you are not using the Author's database, update your database name(s) in lines: 345-360 -# -# katzlab$ python StopFrequency.py YourFastaFile.fasta -# -# -#------------------------------- Interpretation of Results -------------------------------# -# -# FORMATTED BELOW WITH TEXTWRANGLER... -# -# Example output using CILIATE (TGA) genetic Code (NOTE THE In-Frame Densities): -# -# Stop Codon Number_of_Seqs_Analyzed In-frame TAG In-frame TGA In-frame TAA Total Codons In-frame TAG density In-frame TGA density In-frame TAA density -# TGA 341 14 0 22 113156 1.2 0 0.92 -# TAG 424 0 0 34 140085 0 0 0.78 -# TAA 205 14 0 0 16714 0.84 0 0 -# Summary 970 28 0 56 269955 2.04 0 1.7 -# -# VALUES in summary line (OR SUM of Density) that are > 1.5 likely indicate that the STOP -# codon has been reassigned... in the case above, TAG and TAA look like they have been -# reassigned. -# -# -# Example output using UNIVERSAL genetic Code (NOTE THE In-Frame Densities): -# -# Stop Codon Number_of_Seqs_Analyzed In-frame TAG In-frame TGA In-frame TAA Total Codons In-frame TAG density In-frame TGA density In-frame TAA density -# TGA 341 1 0 2 113156 0.2 0 0.05 -# TAG 424 0 2 4 140085 0 0 0.08 -# TAA 205 1 0 0 16714 0.04 0 0 -# Summary 970 2 2 6 269955 0.15 0 0.06 -# -# VALUES in summary line (OR SUM of Density) that are > 0.5 likely indicate that the STOP -# codon still acts as STOP... in the case above, TAG, TGA and TAA look like they still behave -# as a stop codon. -# -# THIS IS A ROUGH GUIDE FOR INTERPRETING THE RESULTS!!!! BE VERY VERY WARY! NUMBER OF TOTAL -# SEQUENCES AND TOTAL CODONS OBSERVED ARE IMPORTANT (TOO FEW AND ANY INTERPRETATION IS DEVOID -# OF ANY MEANING).