diff --git a/Examples/commands/1-Annotate.sh b/Examples/commands/1-Annotate.sh deleted file mode 100644 index 0cbf1f761f09afee7b9582ff6aa89024d743f211..0000000000000000000000000000000000000000 --- 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 0000000000000000000000000000000000000000..4021c88ec99c02f840c5d6d5c94dedd415137245 --- /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 0342cee5cc4dc3a638fbc81eb5145d03fecb0675..0000000000000000000000000000000000000000 --- 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 d44e764fcd874ec3c12e02ce97a5dcac3400e201..0000000000000000000000000000000000000000 --- 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 0000000000000000000000000000000000000000..7b82819d9c52f958f7a3c97d1c227ae5bf3c8000 --- /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 1cd6bfc18825adcb94985fac6e06af269f70dd43..0000000000000000000000000000000000000000 --- 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 0000000000000000000000000000000000000000..e0b42c83f96f1806ebf0e5364910da40ea59c8fe --- /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 0000000000000000000000000000000000000000..81eb407d93173093bef0ff5f489cac0d336e564b --- /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 f5e8cdbbf4fbf05a74225a6789bbe2c56fd72145..0000000000000000000000000000000000000000 --- 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 0000000000000000000000000000000000000000..db0770316a7feaadf19d50d6b7a3563ea42dc696 --- /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