diff --git a/Examples/commands/3-Pangenome.sh b/Examples/commands/3-Pangenome.sh index 2fb73fd135c5683358f97494bfa62c42475999b2..cd7e42542366aaf45c226ebd41dfcd6fd86f1ce3 100644 --- a/Examples/commands/3-Pangenome.sh +++ b/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 diff --git a/Examples/commands/4-Corepers.sh b/Examples/commands/4-Corepers.sh index af619fc0f78c70b509b29df1a9f69655614d4b34..c818f14283c897513ab1dd60b3cfff00e6225b67 100644 --- a/Examples/commands/4-Corepers.sh +++ b/Examples/commands/4-Corepers.sh @@ -1,8 +1,8 @@ # 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 diff --git a/Examples/commands/5-Align.sh b/Examples/commands/5-Align.sh index 00e43f813ad6659621d93c0251f093fd7877f671..ea710648091ebf2ae224c7b5f9c0e595ef33bf21 100644 --- a/Examples/commands/5-Align.sh +++ b/Examples/commands/5-Align.sh @@ -1,5 +1,5 @@ # 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 diff --git a/Examples/commands/6-Tree.sh b/Examples/commands/6-Tree.sh index d03a3ede9a8114ac169edd99d1c52df8f562d003..1e5451a156dd8e53de75d83580ae45106fd01b7c 100644 --- a/Examples/commands/6-Tree.sh +++ b/Examples/commands/6-Tree.sh @@ -1,5 +1,5 @@ # 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 diff --git a/doc/source/examples.rst b/doc/source/examples.rst index e7d7bbe58295fedb59bb2efdda80f2e474a2745e..1c97c635f8a8e3c5afffada58d848867fafb1415 100755 --- a/doc/source/examples.rst +++ b/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).