update command lines for all examples

Examples/commands/3-Pangenome.sh

@@ -2,4 +2,4 @@
 PanACoTA pangenome -l Examples/2-res-prokka/LSTINFO-list_genomes.lst -n GENO3 -d Examples/2-res-prokka/Proteins -i 0.8 -o Examples/3-pangenome
 
 # to run only pangenome step of the example
-PanACoTA pangenome -l Examples/input_files/pan-input/LSTINFO-list_genomes.lst -n GENO3 -d Examples/input_files/pan-input/Proteins -i 0.8 -o Examples/3-pangenome
+PanACoTA pangenome -l Examples/input_files/pan-input/LSTINFO-list_genomes.lst -n GENO3 -d Examples/input_files/pan-input/Proteins -i 0.8 -o Examples/3-pangenome-alone

Examples/commands/4-Corepers.sh

 # core genome
-PanACoTA corepers -p Examples/3-pangenome/PanGenome-GENO3.All.prt-clust-0.8-mode1_<date>.tsv.lst -o Examples/4-corepers
+PanACoTA corepers -p Examples/3-pangenome/PanGenome-GENO3.All.prt-clust-0.8-mode1.lst -o Examples/4-corepers
 
 # strict persistent at 95%
-PanACoTA corepers -p Examples/3-pangenome/PanGenome-GENO3.All.prt-clust-0.8-mode1_<date>.tsv.lst -o Examples/4-corepers -t 0.95
+PanACoTA corepers -p Examples/3-pangenome/PanGenome-GENO3.All.prt-clust-0.8-mode1.lst -o Examples/4-corepers0.95 -t 0.95
 
 # run only coregenome step from example
-PanACoTA corepers -p Examples/input_files/core-input/PanGenome-example.lst -o Examples/4-corepers
\ No newline at end of file
+PanACoTA corepers -p Examples/input_files/core-input/PanGenome-example.lst -o Examples/4-corepers-alone
\ No newline at end of file

Examples/commands/5-Align.sh

 # run example (after running annotate, pan and core steps)
-PanACoTA align -c Examples/4-corepers/PersGenome_<pangenome-filename>_1.lst -l Examples/2-res-prokka/LSTINFO-list_genomes.lst -n GENO3_1 -d Examples/2-res-prokka -o Examples/5-align
+PanACoTA align -c Examples/4-corepers/PersGenome_PanGenome-GENO3.All.prt-clust-0.8-mode1.lst-all_1.lst -l Examples/2-res-prokka/LSTINFO-list_genomes.lst -n GENO3_1 -d Examples/2-res-prokka -o Examples/5-align
 
 # only run align step of example
 PanACoTA align -c Examples/input_files/align-input/coregenome-example.lst -l Examples/input_files/pan-input/LSTINFO-list_genomes.lst -n GENO3_1 -d Examples/input_files/pan-input -o Examples/5-align
\ No newline at end of file

Examples/commands/6-Tree.sh

 # run example after running all other steps (annotate, pan, core, align)
-PanACoTA tree -a Examples/5-align/Phylo-GENO3_1/GENO3_1.grp.aln -o Examples/6-tree
+PanACoTA tree -a Examples/5-align/Phylo-GENO3_1/GENO3_1.nucl.grp.aln -o Examples/6-tree
 
 # run only tree step
-PanACoTA tree -a Examples/input_files/tree-input/GENO3_1.nucl.grp.aln -o Examples/6-tree
\ No newline at end of file
+PanACoTA tree -a Examples/input_files/tree-input/GENO3_1.nucl.grp.aln -o Examples/6-tree-alone
\ No newline at end of file

doc/source/examples.rst

@@ -205,7 +205,7 @@ If you used the same dataset and parameters as in this file, you should get a co
 
 If you want a persistent genome, specify the required :ref:`options<docorepers>` (minimum percentage of genomes in a family to be considered as persistent, allowing or not multi/mixed families...). For example, for a strict persistent genome at 95%::
 
-    PanACoTA corepers -p Examples/3-pangenome/PanGenome-GENO3.All.prt-clust-0.8-mode1.lst -o Examples/4-corepers -t 0.95
+    PanACoTA corepers -p Examples/3-pangenome/PanGenome-GENO3.All.prt-clust-0.8-mode1.lst -o Examples/4-corepers0.95 -t 0.95
 
 The output file will be ``Examples/4-corepers/PersGenome_<pangenome-filename>_0.95.lst``, and will contain the same 6 families (95% of 3 genomes is all genomes).