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Headers in 4_InFrameStopCodonEstimator.py

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Auden Cote-L'Heureux 2024-01-20 13:58:41 -05:00 committed by GitHub
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PTL1/Transcriptomes/Scripts/4_InFrameStopCodonEstimator.py
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@ -9,6 +9,43 @@
# if unsure. This step can be skipped if genetic codes were input from the beginning. This # 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. # 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 import argparse, os, sys
from argparse import RawTextHelpFormatter,SUPPRESS from argparse import RawTextHelpFormatter,SUPPRESS
from distutils import spawn from distutils import spawn
@ -720,52 +757,3 @@ def main():
next_script(args) next_script(args)
main() 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).