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