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Updating header in 1b_CrossPlateContamination.py

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Auden Cote-L'Heureux 2024-01-16 11:55:23 -05:00 committed by GitHub
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commit e9286e7d7a
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1 changed files with 7 additions and 10 deletions
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PTL1/Transcriptomes/Scripts/1b_CrossPlateContamination.py
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@ -1,10 +1,11 @@
#!/usr/bin/python3 # Last updated 2/23/2022
__author__ = 'Jean-David Grattepanche'
__version__ = 'ACL fixed sequence naming issue Feb 23, 2022'
__email__ = 'jeandavid.grattepanche@gmail.com'
# This script is intended to remove intra-plate contamination
# by removing sequences with low coverage relative to other
# very similar sequences from samples sequenced on the same
# plate.
# Before running this script, you must run Script 1a.
import sys import sys
import os import os
@ -55,8 +56,6 @@ def sort_cluster(folder, listtaxa, minlen, conspecific_names):
print("CLUSTER sequences that overlap at least 70%") print("CLUSTER sequences that overlap at least 70%")
os.system('vsearch --cluster_fast ' + '/'.join(folder.split('/')[:-1]) + '/forclustering.fasta --strand both --query_cov '+str(seqcoverage)+' --id '+str(toosim) +' --uc ' + '/'.join(folder.split('/')[:-1]) + '/clusteringresults_vsearch/results_forclustering.uc --threads 60' ) os.system('vsearch --cluster_fast ' + '/'.join(folder.split('/')[:-1]) + '/forclustering.fasta --strand both --query_cov '+str(seqcoverage)+' --id '+str(toosim) +' --uc ' + '/'.join(folder.split('/')[:-1]) + '/clusteringresults_vsearch/results_forclustering.uc --threads 60' )
#input2 = open('/'.join(folder.split('/')[:-1]) + '/clusteringresults_vsearch/results_forclustering.uc','r')
#input2 = open('/Output_PostClusterBackup/clusteringresults_vsearch/results_forclustering.uc','r')
cluster_output = '/'.join(folder.split('/')[:-1]) + '/clusteringresults_vsearch/results_forclustering.uc' cluster_output = '/'.join(folder.split('/')[:-1]) + '/clusteringresults_vsearch/results_forclustering.uc'
out2 = open('/'.join(folder.split('/')[:-1]) + '/fastatokeep.fas','w+') out2 = open('/'.join(folder.split('/')[:-1]) + '/fastatokeep.fas','w+')
out3 = open('/'.join(folder.split('/')[:-1]) + '/fastatoremoved.fas','w+') out3 = open('/'.join(folder.split('/')[:-1]) + '/fastatoremoved.fas','w+')
@ -67,13 +66,11 @@ def sort_cluster(folder, listtaxa, minlen, conspecific_names):
if row2.split('\t')[0] == 'C' and int(row2.split('\t')[2]) < 2: # keep all unique sequences if row2.split('\t')[0] == 'C' and int(row2.split('\t')[2]) < 2: # keep all unique sequences
out2.write('>'+row2.split('\t')[8] + '\n' + str(fastadict[row2.split('\t')[8]])+ '\n') out2.write('>'+row2.split('\t')[8] + '\n' + str(fastadict[row2.split('\t')[8]])+ '\n')
if row2.split('\t')[0] == 'C' and int(row2.split('\t')[2]) > 1: # create another dictionary if row2.split('\t')[0] == 'C' and int(row2.split('\t')[2]) > 1: # create another dictionary
# print("create dico: ", row2.split('\t')[8])
clustdict.setdefault(row2.split('\t')[8], [row2.split('\t')[8]]) clustdict.setdefault(row2.split('\t')[8], [row2.split('\t')[8]])
clustlist.append(row2.split('\t')[8]) clustlist.append(row2.split('\t')[8])
for row3 in open(cluster_output, 'r'): for row3 in open(cluster_output, 'r'):
if row3.split('\t')[0] == 'H': if row3.split('\t')[0] == 'H':
# print("add dico: ", row3.split('\t')[9], row3.split('\t')[8])
clustdict[row3.split('\t')[9].replace('\n','')].append(row3.split('\t')[8].replace('\n','')) clustdict[row3.split('\t')[9].replace('\n','')].append(row3.split('\t')[8].replace('\n',''))
clustline[row3.split('\t')[8].replace('\n','')] = row3.replace('\n','') clustline[row3.split('\t')[8].replace('\n','')] = row3.replace('\n','')
clustline[row3.split('\t')[9].replace('\n','')] = row3.replace('\n','') clustline[row3.split('\t')[9].replace('\n','')] = row3.replace('\n','')
@ -88,7 +85,7 @@ def sort_cluster(folder, listtaxa, minlen, conspecific_names):
clustered = seq.replace('\n','') clustered = seq.replace('\n','')
Covclustered = int(clustered.split('_Cov')[1]) Covclustered = int(clustered.split('_Cov')[1])
clustered8dig = ('_').join(clustered.split('_')[0:3])[:-2] clustered8dig = ('_').join(clustered.split('_')[0:3])[:-2]
# print(master8dig, Covmaster, '//', clustered8dig, Covclustered)
if float(Covmaster/Covclustered) < 10: if float(Covmaster/Covclustered) < 10:
out2.write('>'+clustered + '\n' + str(fastadict[clustered])+ '\n') out2.write('>'+clustered + '\n' + str(fastadict[clustered])+ '\n')
i +=1 i +=1