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Commit 4d18481f authored by Amandine  PERRIN's avatar Amandine PERRIN
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update command lines for all examples

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...@@ -2,4 +2,4 @@ ...@@ -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 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 # 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
# core genome # 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% # 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 # run only coregenome step from example
PanACoTA corepers -p Examples/input_files/core-input/PanGenome-example.lst -o Examples/4-corepers PanACoTA corepers -p Examples/input_files/core-input/PanGenome-example.lst -o Examples/4-corepers-alone
\ No newline at end of file \ No newline at end of file
# run example (after running annotate, pan and core steps) # 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 # 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 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
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# run example after running all other steps (annotate, pan, core, align) # 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 # run only tree step
PanACoTA tree -a Examples/input_files/tree-input/GENO3_1.nucl.grp.aln -o Examples/6-tree PanACoTA tree -a Examples/input_files/tree-input/GENO3_1.nucl.grp.aln -o Examples/6-tree-alone
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...@@ -205,7 +205,7 @@ If you used the same dataset and parameters as in this file, you should get a co ...@@ -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%:: 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). 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).
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