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Updating header in 2b_Identify_Proks.py

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PTL1/Transcriptomes/Scripts/2b_Identify_Proks.py
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#!/usr/bin/env python3.5
# Last updated Sept. 2023
# Authors: Xyrus Maurer-Alcala and Auden Cote-L'Heureux
##__Updated__: 18_08_2017
##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com
##__Usage__: python 2b_remove_Bact.py --help
# This script is intended to identify likely prokarotic (contaminant) sequences. It does
# this by similarity-searching against a reference database of eukaryote and prokaryote
# sequences, and it labels the output sequences with an "E" (likely eukaryotic), "P" (likely
# prokaryotic) or "U" (Unknown) in the sequence ID. This is done by comparing e-values: if
# a sequence hits a eukaryotic sequence with an e-value >100 times that of its best hit
# to a prokaryotic sequence, it is labeled with an "E"; if it's best hit to a prokaryotic
# sequence has an e-value >1000 times that of its best hit to a eukaryotic sequence, it is
# labeled with a "P". Anything else gets a "U". This script should be run as part of the
# PhyloToL version 6 Part 1 pipeline using the script wrapper.py.
##########################################################################################
## This script is intended to identify and isolate SSU/LSU sequences ##
## 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 < 300bp) with ContigFilterPlusStats.py ##
## 3. Have the Databases set up correctly (e.g. with BLAST or Diamond) and in their ##
## respective folders! See the manual if you need help ##
## 4. Run removeSSU.py on your Fasta file ##
## ##
## COMMAND Example Below ##
## ##
## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ##
## ##
## Next Script(s) to Run: ##
## 3_CountOGsDiamond.py ##
## ##
##########################################################################################
# Prior to running this script, ensure that you have run scripts 1a (and optionally
# script 1b) and 2a, and that your prokaryote and reference databases (or the default
# ones provided on the GitHub) is in the proper database folder
# (Databases/BvsE/eukout.dmnd and micout.dmnd).
import argparse, os, sys