diff --git a/README.md b/README.md index 4f4b343..8aaf3c2 100644 --- a/README.md +++ b/README.md @@ -57,3 +57,8 @@ python src/simulation_reads.py -n 25 -m 25 -p 5 -k 1 -s 0 -d 0.1 -a 0.001 -b 0.0 An example of usage is as follows. $ python src/condor.py -i data/sample/overview_character_matrix.csv -a 0.0018 -b 0.001 -k 1 -r data/sample/overview_read_count.csv -v data/sample/overview_variant_count.csv -o data/sample/overview + +**An example of usage with only bash command** +``` +bash condor.sh data/sample/overview_character_matrix.csv data/sample/overview_read_count.csv data/sample/overview_variant_count.csv data/sample/overview +``` \ No newline at end of file diff --git a/condor.sh b/condor.sh new file mode 100644 index 0000000..4009081 --- /dev/null +++ b/condor.sh @@ -0,0 +1,39 @@ + +#inspired from SCARLET[https://github.com/raphael-group/scarlet] + +if [ "$#" -le 3 ]; then + echo """ + + usage: condor.py [-h] [-i I] [-r R] [-v V] [-s S] [-a A] [-b B] [--ado ADO] [-k K] -o O [-t T] + +optional arguments: + -h, --help show this help message and exit + -i I csv file with mutation matrix and cluster id + -r R csv file with total read count matrix + -v V csv file with variant read count matrix + -s S file containing list of SNPs + -a A false positive error rate [0.001] + -b B false negative error rate [0.001] + --ado ADO precision parameter for ADO + -k K maximum number of losses for an SNV + -o O output prefix + -t T time limit in seconds [1800] + + """ + exit 1 +fi + + +character_matrix=$1 +read_count=$2 +variant_count=$3 +output_prefix=$4 + + +DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )" + +python $DIR/src/condor.py -i $character_matrix -a 0.0018 -b 0.001 -k 1 -r $read_count -v $variant_count -o $output_prefix + + +dot -Tpdf ${output_prefix}_tree.dot -o ${output_prefix}_tree.pdf -v +dot -Tpdf ${output_prefix}_tree_without_cells.dot -o ${output_prefix}_tree_without_cells.pdf -v