YuuMJ1997/EukPhylo
1
0
Fork 0
mirror of http://43.156.76.180:8026/YuuMJ/EukPhylo.git synced 2025-12-27 12:30:25 +08:00
Code Issues Packages Projects Releases Wiki Activity

Updating header in 2b_Identify_Proks.py

Browse Source
This commit is contained in:
Auden Cote-L'Heureux 2024-01-16 14:32:26 -05:00 committed by GitHub
parent e3077b1caa
commit c77e63eb74
No known key found for this signature in database
GPG Key ID: B5690EEEBB952194
1 changed files with 15 additions and 23 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

38
PTL1/Transcriptomes/Scripts/2b_Identify_Proks.py
View File

@ -1,28 +1,20 @@
#!/usr/bin/env python3.5 # Last updated Sept. 2023
# Authors: Xyrus Maurer-Alcala and Auden Cote-L'Heureux
##__Updated__: 18_08_2017 # This script is intended to identify likely prokarotic (contaminant) sequences. It does
##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com # this by similarity-searching against a reference database of eukaryote and prokaryote
##__Usage__: python 2b_remove_Bact.py --help # 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.
########################################################################################## # Prior to running this script, ensure that you have run scripts 1a (and optionally
## This script is intended to identify and isolate SSU/LSU sequences ## # script 1b) and 2a, and that your prokaryote and reference databases (or the default
## Prior to running this script, ensure the following: ## # ones provided on the GitHub) is in the proper database folder
## ## # (Databases/BvsE/eukout.dmnd and micout.dmnd).
## 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 ##
## ##
##########################################################################################
import argparse, os, sys import argparse, os, sys