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Updating headers in 6_FilterPartials.py

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Auden Cote-L'Heureux 2024-01-26 10:43:04 -05:00 committed by GitHub
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PTL1/Transcriptomes/Scripts/6_FilterPartials.py
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#!/usr/bin/env python3.5
##__Updated__: 2023-09-27 by Auden Cote-L'Heureux
##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com; xyrus.maurer-alcala@izb.unibe.ch
##__Usage__: python 6_FilterPartials.py --help
# Last updated Sept 2023
# Authors: Xyrus Maurer-Alcala and Auden Cote-L'Heureux
##################################################################################################
## This script is intended to remove incomplete transcripts that have a more complete mate ##
## ##
## Prior to running this script, ensure the following: ##
## ##
## 1. You have assembled your transcriptome and COPIED the 'assembly' file ##
## (contigs.fasta, or scaffolds.fasta) to the PostAssembly Folder ##
## 2. Removed small sequences (usually sequences < 200bp) ##
## 3. Removed SSU/LSU sequences from your Fasta File ##
## 4. Classified your sequences as Strongly Prokaryotic/Eukaryotic or Undetermined ##
## 5. Classified sequences into OGs ##
## 6. You either know (or have inferred) the genetic code of the organism ##
## 7. You have translated the sequences and checked for the data in the RemovePartials folder ##
## ##
## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ##
## ##
## Next Script(s) to Run: ##
## 7_FinalRename.py ##
## ##
##################################################################################################
# This script is intended to remove incomplete transcripts that have a more complete mate.
# First, all sequences shorter than 33% or longer than 150% the average length of sequences
# from the same OG in the Hook database are removed. Then, for each transcriptomic sample,
# all sequences within an OG are compared at the nucleotide level to the sequence with the
# highest “score” (defined as k-mer coverage multiplied by length). The script should be run
# as part of the PhyloToL 6 Part 1 pipeline using the script wrapper.py. It requires that the
# structure of the 'Output' folder be as output by script 5, and that the Databases/db_OG folder
# contains a .fasta file containing all amino acid sequences in the OG reference database (Hook)
# with the same file name (until the extension) as the .dmnd file for the reference database used
# in script 3.
#Dependencies
from Bio import SeqIO
from Bio.Seq import Seq
from statistics import mean