From 5f28d4447f3a3bb1cdac0cb8459ed57c8d451792 Mon Sep 17 00:00:00 2001
From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com>
Date: Fri, 29 Sep 2023 13:20:11 -0400
Subject: [PATCH] Delete
 PTL1/Transcriptomes/Scripts/6b_update_cov_post_removepartials.py

---
 .../6b_update_cov_post_removepartials.py      | 88 -------------------
 1 file changed, 88 deletions(-)
 delete mode 100644 PTL1/Transcriptomes/Scripts/6b_update_cov_post_removepartials.py

diff --git a/PTL1/Transcriptomes/Scripts/6b_update_cov_post_removepartials.py b/PTL1/Transcriptomes/Scripts/6b_update_cov_post_removepartials.py
deleted file mode 100644
index 6d248b1..0000000
--- a/PTL1/Transcriptomes/Scripts/6b_update_cov_post_removepartials.py
+++ /dev/null
@@ -1,88 +0,0 @@
-#!/usr/bin/python
-from __future__ import print_function
-
-__author__ = "Jean-David Grattepanche"
-__version__ = "2, August 28, 2017"
-__email__ = "jeandavid.grattepanche@gmail.com"
-
-
-import sys
-import os
-import re
-import time
-import string
-import os.path
-from Bio import SeqIO
-from sys import argv
-
-def Addcoverage(code):
-	seqfolder = code
-	all_output_folder = '/'.join(code.split('/')[:-1])
-	code = code.split('/')[-1]
-	
-	covupd = {}
-	for seqcoll in open(seqfolder + '/' + code + '_SeqPairsAbove98.txt','r'):
-		CL = 0
-		for transc in seqcoll.split('\t'):
-			if CL == 0:
-				reftrans = ('_').join(transc.split('_')[1:])
-			coverage = int(transc.split('Cov')[1].split('_')[0])
-			Length = int(transc.split('Len')[1].split('_')[0])
-			CL += coverage * Length
-		covupd[reftrans] = CL 
-
-	if os.path.isdir(seqfolder + '/Updated_Coverage/') != True:
-		os.system('mkdir ' + seqfolder + '/Updated_Coverage/')
-	if os.path.isdir(seqfolder + '/Updated_Coverage/SpreadSheets/') != True:
-		os.system('mkdir ' + seqfolder + '/Updated_Coverage/SpreadSheets/')
-
-	for spreadsh in os.listdir(seqfolder + '/Processed/SpreadSheets/'):
-		if spreadsh.endswith('.tsv'):
-			outtsvtokeep = open(seqfolder + '/Updated_Coverage/SpreadSheets/' + spreadsh.split('Final')[0] + 'UC.Final' + spreadsh.split('Final')[1],'w+')
-			for row in open(seqfolder + '/Processed/SpreadSheets/'+ spreadsh, 'r'):
-				if row.split('_Trans')[0] in covupd:
-					og_number = re.split('OG.{1}_', row)[-1][:6]
-					og_prefix = row.split(og_number)[0][-4:]
-					og = og_prefix + og_number
-
-					newcov2 = round(covupd[row.split('_Trans')[0]] / int(row.split('_Len')[1].split('_')[0]))
-					outtsvtokeep.write(row.split('Cov')[0]+'Cov'+str(newcov2)+'_' + og_prefix +row.split(og_prefix)[1].split('_Trans')[0] +'\t' +('\t').join(row.split('\t')[1:]))
-				else: 
-					if 'Trans' in row:
-						outtsvtokeep.write(row.split('_Trans')[0]+ '\t' +('\t').join(row.split('\t')[1:]))
-					else:
-						outtsvtokeep.write(row)
-			outtsvtokeep.close()
-
-	for seqfile in os.listdir(seqfolder + '/Processed'):
-		if seqfile.endswith('.fasta'):
-			outseqtokeep = open(seqfolder + '/Updated_Coverage/' + seqfile.split('Final')[0] + 'UC.Final' + seqfile.split('Final')[1],'w+')
-			for Seq in SeqIO.parse(seqfolder + '/Processed/' + seqfile ,'fasta'):
-				if Seq.description.split('_Trans')[0] not in covupd:
-					outseqtokeep.write('>'+Seq.description.split('_Trans')[0]+ '\n'+str(Seq.seq) +'\n')
-				else:
-					og_number = re.split('OG.{1}_', Seq.description)[-1][:6]
-					og_prefix = Seq.description.split(og_number)[0][-4:]
-					og = og_prefix + og_number
-
-					newcov = round(covupd[Seq.description.split('_Trans')[0]] / int(Seq.description.split('_Len')[1].split('_')[0]))
-					outseqtokeep.write('>'+Seq.description.split('Cov')[0]+'Cov'+str(newcov)+'_' + Seq.description.split(og)[0][-2:] + og + '\n'+str(Seq.seq) +'\n')
-			outseqtokeep.close()
-
-	if os.path.isdir(all_output_folder + '/ToRename') != True:
-		os.system('mkdir ' + all_output_folder + '/ToRename')
-
-	os.system('cp ' + seqfolder + '/Updated_Coverage/*fasta ' + all_output_folder + '/ToRename/')
-	os.system('cp ' + seqfolder + '/Updated_Coverage/SpreadSheets/*tsv ' + all_output_folder + '/ToRename/')
-			
-			
-def main():
-	script, code = argv
-	Addcoverage(code)
-main()
-
-
-
-
-
-