YuuMJ1997/EukPhylo
1
0
Fork 0
mirror of http://43.156.76.180:8026/YuuMJ/EukPhylo.git synced 2025-12-28 00:00:25 +08:00
Code Issues Packages Projects Releases Wiki Activity

Delete PTL1/Transcriptomes/Scripts/6b_update_cov_post_removepartials.py

Browse Source
This commit is contained in:
Auden Cote-L'Heureux 2023-09-29 13:20:11 -04:00 committed by GitHub
parent eb3db88688
commit 5f28d4447f
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
1 changed files with 0 additions and 88 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

88
PTL1/Transcriptomes/Scripts/6b_update_cov_post_removepartials.py
View File

@ -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()