From 45f5b54a75c67f1418feea59396e3477f8e2ef39 Mon Sep 17 00:00:00 2001 From: Amandine PERRIN <amandine.perrin@pasteur.fr> Date: Wed, 2 Sep 2020 11:46:48 +0200 Subject: [PATCH] Add commands for example --- Examples/commands/1-Annotate.sh | 6 ------ Examples/commands/2-Annotate.sh | 9 +++++++++ Examples/commands/2-Pangenome.sh | 2 -- Examples/commands/3-Corepers.sh | 1 - Examples/commands/3-Pangenome.sh | 2 ++ Examples/commands/4-Align.sh | 1 - Examples/commands/4-Corepers.sh | 5 +++++ Examples/commands/5-Corepers.sh | 1 + Examples/commands/5-Tree.sh | 1 - Examples/commands/6-Tree.sh | 1 + 10 files changed, 18 insertions(+), 11 deletions(-) delete mode 100644 Examples/commands/1-Annotate.sh create mode 100644 Examples/commands/2-Annotate.sh delete mode 100644 Examples/commands/2-Pangenome.sh delete mode 100644 Examples/commands/3-Corepers.sh create mode 100644 Examples/commands/3-Pangenome.sh delete mode 100644 Examples/commands/4-Align.sh create mode 100644 Examples/commands/4-Corepers.sh create mode 100644 Examples/commands/5-Corepers.sh delete mode 100644 Examples/commands/5-Tree.sh create mode 100644 Examples/commands/6-Tree.sh diff --git a/Examples/commands/1-Annotate.sh b/Examples/commands/1-Annotate.sh deleted file mode 100644 index 0cbf1f76..00000000 --- a/Examples/commands/1-Annotate.sh +++ /dev/null @@ -1,6 +0,0 @@ -# With prokka -PanACoTA annotate -d Examples/genomes_init -r Examples/1-res-prokka -l Examples/input_files/list_genomes.lst -n EXAM --l90 3 --nbcont 10 - - -# With prodigal -PanACoTA annotate -d Examples/genomes_init -r Examples/1-res-prodigal -l Examples/input_files/list_genomes.lst -n EXAM --l90 3 --prodigal --small diff --git a/Examples/commands/2-Annotate.sh b/Examples/commands/2-Annotate.sh new file mode 100644 index 00000000..4021c88e --- /dev/null +++ b/Examples/commands/2-Annotate.sh @@ -0,0 +1,9 @@ +# Only QC +PanACoTA annotate -d Examples/genomes_init -l Examples/input_files/list_genomes.lst -r Examples/2-res-QC -Q + +# With prokka +PanACoTA annotate -d Examples/genomes_init -r Examples/2-res-prokka -l Examples/input_files/list_genomes.lst -n GENO --l90 3 --nbcont 10 + + +# With prodigal +PanACoTA annotate -d Examples/genomes_init -r Examples/2-res-prodigal -l Examples/input_files/list_genomes.lst -n GENO --l90 3 --prodigal --small diff --git a/Examples/commands/2-Pangenome.sh b/Examples/commands/2-Pangenome.sh deleted file mode 100644 index 0342cee5..00000000 --- a/Examples/commands/2-Pangenome.sh +++ /dev/null @@ -1,2 +0,0 @@ -PanACoTA pangenome -l Examples/1-res-Annotate/LSTINFO-list_genomes.lst -n EXAMPLE4 -d Examples/1-res-Annotate/Proteins -i 0.8 -o Examples/2-res-pangenome - diff --git a/Examples/commands/3-Corepers.sh b/Examples/commands/3-Corepers.sh deleted file mode 100644 index d44e764f..00000000 --- a/Examples/commands/3-Corepers.sh +++ /dev/null @@ -1 +0,0 @@ -PanACoTA corepers -p Examples/2-res-pangenome/PanGenome-EXAMPLE4.All.prt-clust-0.8-mode1_2019-02-12_13-25-01.tsv.lst diff --git a/Examples/commands/3-Pangenome.sh b/Examples/commands/3-Pangenome.sh new file mode 100644 index 00000000..7b82819d --- /dev/null +++ b/Examples/commands/3-Pangenome.sh @@ -0,0 +1,2 @@ +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 + diff --git a/Examples/commands/4-Align.sh b/Examples/commands/4-Align.sh deleted file mode 100644 index 1cd6bfc1..00000000 --- a/Examples/commands/4-Align.sh +++ /dev/null @@ -1 +0,0 @@ -PanACoTA align -c Examples/3-coregenome/PersGenome_PanGenome-EXAMPLE4.All.prt-clust-0.8-mode1_2019-02-12_13-25-01.tsv.lst_1.lst -l Examples/1-res-Annotate/LSTINFO-list_genomes.lst -d Examples/1-res-Annotate/ -o Examples/4-Algn -n EXAMPLE4 diff --git a/Examples/commands/4-Corepers.sh b/Examples/commands/4-Corepers.sh new file mode 100644 index 00000000..e0b42c83 --- /dev/null +++ b/Examples/commands/4-Corepers.sh @@ -0,0 +1,5 @@ +# core genome +PanACoTA corepers -p Examples/3-pangenome/PanGenome-GENO3.All.prt-clust-0.8-mode1_<date>.tsv.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 diff --git a/Examples/commands/5-Corepers.sh b/Examples/commands/5-Corepers.sh new file mode 100644 index 00000000..81eb407d --- /dev/null +++ b/Examples/commands/5-Corepers.sh @@ -0,0 +1 @@ +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 diff --git a/Examples/commands/5-Tree.sh b/Examples/commands/5-Tree.sh deleted file mode 100644 index f5e8cdbb..00000000 --- a/Examples/commands/5-Tree.sh +++ /dev/null @@ -1 +0,0 @@ -PanACoTA tree -a Examples/4-Algn/Phylo-EXAMPLE4/EXAMPLE4.grp.aln diff --git a/Examples/commands/6-Tree.sh b/Examples/commands/6-Tree.sh new file mode 100644 index 00000000..db077031 --- /dev/null +++ b/Examples/commands/6-Tree.sh @@ -0,0 +1 @@ +PanACoTA tree -a Examples/5-align/Phylo-GENO3_1/GENO3_1.grp.aln -o Examples/6-tree \ No newline at end of file -- GitLab