Author: Andreas Tille <tille@debian.org>
Last-Update: Mon, 21 Jan 2019 09:01:19 +0100
Description: Result of 2to3

--- a/scripts/filter_out_using_MAF.py
+++ b/scripts/filter_out_using_MAF.py
@@ -2,8 +2,8 @@ import sys
 import gzip
 
 if len(sys.argv)<3:
-    print "This tool filters out discoSnp prediction having a minor allele frequency lower than a provided threshold for ALL datasets."
-    print "python filter_out_using_MAF.py \".fa from discoSnp\" \"MAF threshold\""
+    print("This tool filters out discoSnp prediction having a minor allele frequency lower than a provided threshold for ALL datasets.")
+    print("python3 filter_out_using_MAF.py \".fa from discoSnp\" \"MAF threshold\"")
     sys.exit()
 
 
@@ -52,7 +52,7 @@ while True:
             break
     
     if to_output:
-        print (comment1,path1,comment2,path2,)
+        print((comment1,path1,comment2,path2,))
     
       
             
--- a/scripts/ClassVCF_creator.py
+++ b/scripts/ClassVCF_creator.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 ###############################################
 #Dresscode : class : uppercase
@@ -197,7 +197,7 @@ class VARIANT():
 #---------------------------------------------------------------------------------------------------------------------------                                                   
         def RetrievePolymorphismFromHeader(self):
                 '''Gets from the dicoAllele all the positions, and the nucleotides for each variant '''
-                for key,(posD,ntUp,ntLow) in self.dicoAllele.items(): #Goes through the dictionary of parsed header
+                for key,(posD,ntUp,ntLow) in list(self.dicoAllele.items()): #Goes through the dictionary of parsed header
                         self.upper_path.listPosForward.append(int(posD)+1)
                         self.lower_path.listPosForward.append(int(posD)+1)
                         self.upper_path.listPosReverse.append(len(self.upper_path.seq)-int(posD))
@@ -894,7 +894,7 @@ class INDEL(VARIANT):
                         else:
                                 self.longestSequenceForward=ReverseComplement(self.upper_path.seq)
                                 self.longestSequenceReverse = self.upper_path.seq
-                for key,(posD,ind,amb) in self.dicoAllele.items():#Goes through the dictionary of parsed header
+                for key,(posD,ind,amb) in list(self.dicoAllele.items()):#Goes through the dictionary of parsed header
                         #In case of forward strand mapped
                         #we return the disco indel + the lefmost nucleotide before the indel (by taking into account the ambiguity
                         self.upper_path.listPosForward.append(int(posD)-int(amb))
--- a/scripts/discoSnp++_to_csv.py
+++ b/scripts/discoSnp++_to_csv.py
@@ -1,7 +1,7 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 import sys
 if len(sys.argv) !=2:
-    sys.stdout.write("Mandatory: python discoSnp_to_csv.py prefix_coherent_k_kval_c_cval.fa\n")
+    sys.stdout.write("Mandatory: python3 discoSnp_to_csv.py prefix_coherent_k_kval_c_cval.fa\n")
     sys.stdout.write("This program formats the .fa to .csv format by puting each couple of .fa sequence (4 lines = 2 comments + 2 nucleotide sequences) into one line, replacing the '|' character by spaces and removing the CX_ formating")
     sys.exit(1)
 
@@ -64,7 +64,7 @@ while 1:
         i+=1
     sys.stdout.write( com2_tab[i][:-1]+",")
     
-    print (data1_2,)
+    print((data1_2,))
     
     
     
--- a/scripts/filterOnBestDP_multiple_variant_at_same_pos.py
+++ b/scripts/filterOnBestDP_multiple_variant_at_same_pos.py
@@ -1,7 +1,7 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 #To apply on sorted vcf by position
-#Usage : python filterOnBestDP_multiple_variant_at_same_pos.py <vcf_for_igv> > output.vcf
+#Usage : python3 filterOnBestDP_multiple_variant_at_same_pos.py <vcf_for_igv> > output.vcf
 import sys
 import gzip
 import re
@@ -25,7 +25,7 @@ while True:
                 line = vcf_for_igv.readline()
                 if not line: break
         if line.startswith("#"): #We just print the header
-                print (line.rstrip())
+                print((line.rstrip()))
                 continue
         list_line_same_pos.append(line) #list with all the lines 
         pos=int(line.split("\t")[1])  
@@ -61,9 +61,9 @@ while True:
                                                 DP_max=DP
         compt+=1
         if to_output:
-                print (line_to_print.rstrip())
+                print((line_to_print.rstrip()))
         elif line_to_print :
-                print (line_to_print.rstrip())
+                print((line_to_print.rstrip()))
         if out:break         
 vcf_for_igv.close() 
 
--- a/scripts/filter_out_using_ratio_of_covered_files.py
+++ b/scripts/filter_out_using_ratio_of_covered_files.py
@@ -3,7 +3,7 @@ import gzip
 
 if len(sys.argv)<4:
     print ("This tool filters out discoSnp prediction whose number of read sets covering it is lower than a user defined threshold. A set covers a prediction if its coverage in at least one of the two alleles is higher than a user defined threshold")
-    print ("python filter_out_using_ratio_of_covered_files.py \".fa from discoSnp\" \"number of sets threshold\" \"minimal coverage\"")
+    print ("python3 filter_out_using_ratio_of_covered_files.py \".fa from discoSnp\" \"number of sets threshold\" \"minimal coverage\"")
     sys.exit()
 
 
@@ -53,7 +53,7 @@ while True:
         if coverage_high[i]>=minimal_coverage or coverage_low[i]>=minimal_coverage: number_of_covered_sets+=1
     
     if 100*number_of_covered_sets/float(number_of_read_sets)>=ratio_threshold:
-        print (comment1,path1,comment2,path2,)
+        print((comment1,path1,comment2,path2,))
     
       
             
--- a/scripts/functionObjectVCF_creator.py
+++ b/scripts/functionObjectVCF_creator.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 ###############################################
 import os
@@ -199,25 +199,25 @@ def CheckAtDistanceXBestHits(upper_path,
         best_up=1024
         if int(upper_path.mappingPosition)==0 and int(lower_path.mappingPosition)==0:#Checks if paths are unmappped
                 return(".")
-        for position,(nbMismatch,cigarcode) in posUp.items(): 
+        for position,(nbMismatch,cigarcode) in list(posUp.items()): 
                 if nbMismatch<best_up:
                         best_up=nbMismatch
 
         # get the best mapping distance for lower path 
         best_low=1024
-        for position,(nbMismatch,cigarcode) in posLow.items(): 
+        for position,(nbMismatch,cigarcode) in list(posLow.items()): 
                 if nbMismatch<best_low:
                         best_low=nbMismatch
 
         # get the union of the mapping position at the best mapping positions
         position_set = set()
-        for position,(nbMismatch,cigarcode) in posUp.items():
+        for position,(nbMismatch,cigarcode) in list(posUp.items()):
                 if nbMismatch == best_up:
                         position_set.add(position)
                 if len(position_set) > 1: 
                         return("MULTIPLE")
 
-        for position,(nbMismatch,cigarcode) in posLow.items():
+        for position,(nbMismatch,cigarcode) in list(posLow.items()):
                 if nbMismatch == best_low:
                         position_set.add(position)
                 if len(position_set) > 1: 
--- a/scripts/VCF_creator.py
+++ b/scripts/VCF_creator.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 #*****************************************************************************
 #   VCF_Creator: mapping and VCF creation feature in DiscoSnp++
--- a/scripts/format_phased_variants_for_haplotyping.py
+++ b/scripts/format_phased_variants_for_haplotyping.py
@@ -3,11 +3,11 @@ import sys
 ### first create connected components from disco (-A option)
 #sh from_phased_alleles_to_clusters.sh phased_alleles_read_set_id_1.txt # creates file connected_components_phased_alleles_read_set_id_1.txt
 ### them from the .fa file, the id of the set your interested in (e.g. 1 for phased_alleles_read_set_id_1.txt, this will correspond to C1 coverage in the fa file), the file containing the connected components, and the phased_alleles_read_set_id_X.txt file, generate the fact file
-#python format_phased_variants_for_haplotyping.py mapping_k_31_c_auto_D_100_P_10_b_0_coherent.fa 1 connected_components_phased_alleles_read_set_id_1.txt phased_alleles_read_set_id_1.txt  > phased_alles_read_set_1_facts.txt
+#python3 format_phased_variants_for_haplotyping.py mapping_k_31_c_auto_D_100_P_10_b_0_coherent.fa 1 connected_components_phased_alleles_read_set_id_1.txt phased_alleles_read_set_id_1.txt  > phased_alles_read_set_1_facts.txt
 
 
 if not len(sys.argv)==5:
-    print ("usage: python format_phased_variants_for_haplotyping.py <file coherent.fa> <id number><connected_component_file><phased_allele_file>")
+    print ("usage: python3 format_phased_variants_for_haplotyping.py <file coherent.fa> <id number><connected_component_file><phased_allele_file>")
     print (" * coherent.fa file: the file generated by discoSnp")
     print (" * id number is the id of the read set, for which variants are phased. With i, this corresponds to Ci in the .fa file headers.")
     print (" * connected_component_file: file obtained from \"from_phased_alleles_to_clusters.sh phased_alleles_read_set_id_1.txt\" continaing connected component of phased alleles")
--- a/scripts/remove_non_covered_genotypes.py
+++ b/scripts/remove_non_covered_genotypes.py
@@ -3,7 +3,7 @@ import gzip
 
 if len(sys.argv)<3:
     print ("This tool replaces discoSnp VCF genotypes with DP lower or equal to a threshold to \"./.\"")
-    print ("python remove_non_covered_genotypes.py \".vcf from discoSnp\" \"DP threshold\"")
+    print ("python3 remove_non_covered_genotypes.py \".vcf from discoSnp\" \"DP threshold\"")
     sys.exit()
 
 
@@ -37,4 +37,4 @@ while True:
             toprint+= splitted_geno[j]
             if j<len(splitted_geno)-1: toprint+= ":"
         if i<len(splitted_line): toprint+='\t'
-    print (toprint)
\ No newline at end of file
+    print (toprint)
--- a/scripts/simulations/multiple_samples_simulator.sh
+++ b/scripts/simulations/multiple_samples_simulator.sh
@@ -68,7 +68,7 @@ fi
 
 for p in `seq 1 $num_pop`
 	do
-	python ./random_mut_fasta.py $genome $div_pop > ERASEME_pos_mut_pop"$p"
+	python3 ./random_mut_fasta.py $genome $div_pop > ERASEME_pos_mut_pop"$p"
 
 	#pos random ordering
 	sort -R ERASEME_pos_mut_pop"$p" > ERASEME_pos_mut_random_pop"$p"
@@ -90,7 +90,7 @@ for p in `seq 1 $num_pop`
 		#homozygotes mutations
 		cat ERASEME_pos_mut_random_shared_allpop"$p" ERASEME_pos_mut_random_shared_pop"$p"_s"$i" > ERASEME_pos_mut_random_spe_pop"$p"_and_s"$i"
 		#mutation inducing
-		python ./targeted_mut_fasta_corrected.py "$genome" ERASEME_pos_mut_random_spe_pop"$p"_and_s"$i"
+		python3 ./targeted_mut_fasta_corrected.py "$genome" ERASEME_pos_mut_random_spe_pop"$p"_and_s"$i"
 		mv "$genome"_mut ERASEME_"$genome"_pop"$p"_s"$i"_withhetero.fasta
 		#homozygote and heterozygote mutations
 		nb_line2=`grep "." -c ERASEME_pos_mut_random_shared_pop"$p"_s"$i"`
@@ -99,7 +99,7 @@ for p in `seq 1 $num_pop`
 		head -n +"$nb_homo" ERASEME_pos_mut_random_shared_pop"$p"_s"$i" > ERASEME_pos_mut_random_shared_pop"$p"_s"$i"_homo
 		#population mutationq
 		cat ERASEME_pos_mut_random_shared_allpop"$p" ERASEME_pos_mut_random_shared_pop"$p"_s"$i"_homo > ERASEME_pos_mut_random_spe_pop"$p"_and_s"$i"_homo
-		python ./targeted_mut_fasta_corrected.py "$genome" ERASEME_pos_mut_random_spe_pop"$p"_and_s"$i"_homo
+		python3 ./targeted_mut_fasta_corrected.py "$genome" ERASEME_pos_mut_random_spe_pop"$p"_and_s"$i"_homo
 		mv "$genome"_mut ERASEME_"$genome"_pop"$p"_s"$i"_homo.fasta
 		#READS SIMULATION
 		mutareads_forward ERASEME_"$genome"_pop"$p"_s"$i"_withhetero.fasta pop"$p"_ind"$i"_allele1_err_reads $read_s $read_l 0.01 0 0
--- a/scripts/simulations/targeted_mut_fasta_corrected.py
+++ b/scripts/simulations/targeted_mut_fasta_corrected.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 # 
 
--- a/scripts/from_phased_alleles_to_clusters.sh
+++ b/scripts/from_phased_alleles_to_clusters.sh
@@ -13,7 +13,7 @@ filename=$(basename -- "$file")
 path=$(dirname "${file}")
 
 # FIND THE PATH CONTAINING THE SCRIPT: 
-EDIR=$( python -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) 
+EDIR=$( python3 -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) 
 echo $EDIR
 
 edge_coverage_threshold=0
@@ -77,4 +77,4 @@ then
     exit 1
 fi
 
-echo "Connected components (clusters of variants) from file $file are in $path/connected_components_${filename}"
\ No newline at end of file
+echo "Connected components (clusters of variants) from file $file are in $path/connected_components_${filename}"
--- a/scripts/redundancy_removal_discosnp.py
+++ b/scripts/redundancy_removal_discosnp.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 ###################################
 # from kissnp output: 
--- a/scripts/simulations/random_mut_fasta.py
+++ b/scripts/simulations/random_mut_fasta.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 # 
 
--- a/scripts/create_IGV_compatible_VCF.sh
+++ b/scripts/create_IGV_compatible_VCF.sh
@@ -30,7 +30,7 @@ igvfile=$(basename $vcffile .vcf)"_for_I
 cat $vcffile|grep "#">$igvfile
 #cat $vcffile|grep -v  "#"|sort -k 2n,2n -n|grep -v "^SNP"|grep -v "^INDEL">>$igvfile
 cat $vcffile|grep -v  "#"|sort -k 1,1 -k 2,2n |grep -v "^SNP"|grep -v "^INDEL">>$igvfile # from 2 2 6
-#python $DIR/tools/one2zeroBased_vcf.py $igvfiletemp 
+#python3 $DIR/tools/one2zeroBased_vcf.py $igvfiletemp 
 #cat VCFone2zeroBAsed.vcf >> $igvfile
 #rm -f $igvfiletemp VCFone2zeroBAsed.vcf
 echo -e "... Creation of the vcf file for IGV: done ...==> $igvfile"
--- a/scripts/k3000/K3000_gfa_to_dat.py
+++ b/scripts/k3000/K3000_gfa_to_dat.py
@@ -461,7 +461,7 @@ def main(gfa_file_name):
     '''
     Creation of a DAT file from the graph_plus.gfa GFA file 
     Usage: 
-        python ~/workspace/gatb-discosnp/scripts/k3000/K3000_gfa_to_dat.py graph_plus.gfa > graph_diploid.dat
+        python3 ~/workspace/gatb-discosnp/scripts/k3000/K3000_gfa_to_dat.py graph_plus.gfa > graph_diploid.dat
     '''
     warnings.warn(f"{sys.argv[0]} is not maintenained anymore (May 2020).", DeprecationWarning)
     
--- a/scripts/keep_extensions_disco_file.py
+++ b/scripts/keep_extensions_disco_file.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 ###################################
 # change extensions in uppercase and replace relative positions of SNPs in the header
--- a/scripts/remove_extensions_disco_file.py
+++ b/scripts/remove_extensions_disco_file.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 ###################################
 #Removes extensions in lowercase :
--- a/scripts/validation_scripts/compare_vcf_disco_pos_allele_only.py
+++ b/scripts/validation_scripts/compare_vcf_disco_pos_allele_only.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 # 
 
--- a/scripts/validation_scripts/eval_disco_one_snp_per_locus.py
+++ b/scripts/validation_scripts/eval_disco_one_snp_per_locus.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 # 
 
--- a/scripts/k3000/K3000.py
+++ b/scripts/k3000/K3000.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 #
 '''
--- a/scripts/k3000/K3000_node_ids_to_node_sequences.py
+++ b/scripts/k3000/K3000_node_ids_to_node_sequences.py
@@ -163,7 +163,7 @@ def main():
     Produces a gfa file replacing the node content from int ids of alleles to their sequence
     '''
     if len(sys.argv) !=3:
-        sys.stderr.write("Usage: python K3000_node_ids_to_node_sequences.py graph_plus.gfa compacted_facts.fa > graph_final.gfa\n")
+        sys.stderr.write("Usage: python3 K3000_node_ids_to_node_sequences.py graph_plus.gfa compacted_facts.fa > graph_final.gfa\n")
         sys.exit(0)
     sys.stderr.write("Indexing sequence positions\n")
     header_to_file_position = index_sequences_seek(sys.argv[2])
--- a/scripts/remove_non_biallelic.py
+++ b/scripts/remove_non_biallelic.py
@@ -3,7 +3,7 @@ import gzip
 
 if len(sys.argv)<2:
     print ("This tool removes from discoSnp sorted VCF the locus which are tri-allelic or more")
-    print ("python remove_non_diploids.py \".vcf from discoSnp\" ")
+    print ("python3 remove_non_diploids.py \".vcf from discoSnp\" ")
     sys.exit()
 
 
--- a/discoSnpRAD/post-processing_scripts/README.md
+++ b/discoSnpRAD/post-processing_scripts/README.md
@@ -7,7 +7,7 @@
        * removes variants belonging to a cluster (locus) whose size (nb of variants) is outside the given size range (options `-m` and `-M`)
        * removes variants with rank lower than a given threshold given by option `-r`
        * Usage :  
-       `python filter_by_cluster_size_and_rank.py -i vcf_file [-o new_vcf_file -m 0 -M 150 -r 0.4]`
+       `python3 filter_by_cluster_size_and_rank.py -i vcf_file [-o new_vcf_file -m 0 -M 150 -r 0.4]`
 
    3. **script** `filter_vcf_by_indiv_cov_max_missing_and_maf.py`:
        * replaces individual genotypes that have DP less than the value given by option `-c` by missing genotype `./.`
@@ -15,14 +15,14 @@
        * removes variants (vcf lines) that have a minor allele frequency smaller than the value given by option `-f` 
        * outputs only SNP variants if option `-s`. 
        * Usage :    
-       `python filter_vcf_by_indiv_cov_max_missing_and_maf.py -i vcf_file -o new_vcf_file [-c min_cov -m max_missing -f maf -s] `
+       `python3 filter_vcf_by_indiv_cov_max_missing_and_maf.py -i vcf_file -o new_vcf_file [-c min_cov -m max_missing -f maf -s] `
 
   3. **script** `filter_paralogs.py`:
         * identifies variants (vcf lines) that have a fraction of heterozygous genotypes greater than `x` (not counting missing genotypes)
         * removes variants (vcf lines) that belong to a cluster having a fraction of such variants greater than `y`
         * Example : `x=0.1` and `y= 0.5` and if we consider a cluster to represent a locus. This filter removes loci that have more than 50% of the SNPs that have each more than 10% of heterozygous genotypes.
         * Usage :     
-        `python filter_paralogs.py -i vcf_file -o new_vcf_file [-x 0.1 -y 0.5]`
+        `python3 filter_paralogs.py -i vcf_file -o new_vcf_file [-x 0.1 -y 0.5]`
 
 
 ## Scripts for STRUCTURE analyses :
@@ -30,7 +30,7 @@
    4. **script** `1SNP_per_cluster.py`
         * selects one SNP per cluster (the one with less missing genotypes)
         * Usage :   
-        `python  1SNP_per_cluster.py -i vcf_file -o new_vcf_file`
+        `python3  1SNP_per_cluster.py -i vcf_file -o new_vcf_file`
 
    5. **script** `vcf2structure.sh`    
         * changes the vcf format to a Structure format (input of the software Structure)
@@ -56,13 +56,13 @@ Here is the full pipeline to map the res
 sh [DISCO_DIR]/scripts/run_VCF_creator.sh  -G dm6_masked.fa -p myDiscoSnpRADResult_raw_filtered.fa -e -o temp.vcf
 
 # Adding clustering information (and minimal filtering on cluster size)
-python add_cluster_info_to_mapped_vcf.py -m temp.vcf -u myDiscoSnpRADResult_clustered.vcf -o myDiscoSnpRADResult_mapped.vcf
+python3 add_cluster_info_to_mapped_vcf.py -m temp.vcf -u myDiscoSnpRADResult_clustered.vcf -o myDiscoSnpRADResult_mapped.vcf
 # final vcf is myDiscoSnpRADResult_mapped.vcf
 ```
 
 Additionnally, in a validation context, if one wants to compare variant positions between two such vcf files, the following command will output recall and precision metrics:
 ```
-python [DISCO_DIR]/scripts/validation_scripts/compare_vcf_disco_pos_allele_only.py truth.vcf myDiscoSnpRADResult_mapped.vcf
+python3 [DISCO_DIR]/scripts/validation_scripts/compare_vcf_disco_pos_allele_only.py truth.vcf myDiscoSnpRADResult_mapped.vcf
 ```
 
 
--- a/discoSnpRAD/post-processing_scripts/filter_by_cluster_size_and_rank.py
+++ b/discoSnpRAD/post-processing_scripts/filter_by_cluster_size_and_rank.py
@@ -1,5 +1,4 @@
-
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 
--- a/doc/discoSnp_user_guide.txt
+++ b/doc/discoSnp_user_guide.txt
@@ -299,7 +299,7 @@ See documentation specific to VCF_creato
 Output Analyze
 	From a fasta format to a csv format: If you wish to analyze the results in a tabulated 
 format:
-?	# python output_analyses/discoSnp++_to_csv.py discoSnp++_output.fa
+?	# python3 output_analyses/discoSnp++_to_csv.py discoSnp++_output.fa
 ?	will output a .csv tabulated file containing on each line the content of 4 lines of the .fa, 
 replacing the '|' character by comma ',' and removing the CX_
 Exemples of close SNPs and indels
--- a/run_discoSnp++.sh
+++ b/run_discoSnp++.sh
@@ -66,7 +66,7 @@ e="" # if set to -e: Map variant predict
 graph_reused="Egg62hdS7knSFvF3" # with -g option, we use a previously created graph. 
 
 #EDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
-#EDIR=$( python -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron 
+#EDIR=$( python3 -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron 
 EDIR="/usr"
 
 
--- a/discoSnpRAD/post-processing_scripts/add_cluster_info_to_mapped_vcf.py
+++ b/discoSnpRAD/post-processing_scripts/add_cluster_info_to_mapped_vcf.py
@@ -1,5 +1,4 @@
-
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 import sys
--- a/discoSnpRAD/post-processing_scripts/filter_paralogs.py
+++ b/discoSnpRAD/post-processing_scripts/filter_paralogs.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 
--- a/discoSnpRAD/post-processing_scripts/filter_vcf_by_indiv_cov_max_missing_and_maf.py
+++ b/discoSnpRAD/post-processing_scripts/filter_vcf_by_indiv_cov_max_missing_and_maf.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 ''' ***********************************************
--- a/discoSnpRAD/post-processing_scripts/1SNP_per_cluster.py
+++ b/discoSnpRAD/post-processing_scripts/1SNP_per_cluster.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # -*- coding: utf-8 -*-
 
 
--- a/discoSnpRAD/run_discoSnpRad.sh
+++ b/discoSnpRAD/run_discoSnpRad.sh
@@ -82,7 +82,7 @@ max_missing=0.95
 min_rank=0.4
 
 #EDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
-EDIR=$( python -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron 
+EDIR=$( python3 -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron 
 
 if [ -d "$EDIR/../build/" ] ; then # VERSION SOURCE COMPILED
     read_file_names_bin=$EDIR/../build/bin/read_file_names
@@ -640,7 +640,7 @@ fi
 echo "${yellow}     ############################################################"
 echo "     #################### REDUNDANCY REMOVAL  ###################"
 echo "     ############################################################$reset"
-redundancy_removal_cmd="python $EDIR/../scripts/redundancy_removal_discosnp.py ${kissprefix}_r.fa $k $kissprefix.fa"
+redundancy_removal_cmd="python3 $EDIR/../scripts/redundancy_removal_discosnp.py ${kissprefix}_r.fa $k $kissprefix.fa"
 echo $green${redundancy_removal_cmd}$cyan
 if [[ "$wraith" == "false" ]]; then
    eval ${redundancy_removal_cmd}
--- a/run_discoSnp++_ML.sh
+++ b/run_discoSnp++_ML.sh
@@ -67,7 +67,7 @@ stop_after_kissnp=0
 e=""
 prefix_trash=`head /dev/urandom | tr -dc A-Za-z0-9 | head -c 13 ; echo ''`
 #EDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
-EDIR=$( python -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron 
+EDIR=$( python3 -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron 
 
 
 if [ -d "$EDIR/build/" ] ; then # VERSION SOURCE COMPILED
@@ -839,4 +839,4 @@ if [[ "$wraith" == "false" ]]; then
     fi
     echo -e " Thanks for using discoSnp++ - http://colibread.inria.fr/discoSnp/ - Forum: http://www.biostars.org/t/discoSnp/"
     echo -e "################################################################################################################${reset}"
-fi
\ No newline at end of file
+fi