3) Identification
Once the reads are assigned (or not assigned), the identification is done using the {Strains x Reads} affiliation matrix by an exact optimization step for the selection of a minimum number of strains explaining all the reads.
ORI.py identification -m path/to/matrix.tsv -f path/to/results/from/HowDeSBT -le path/to/length.txt/or/merge_length.txt -l path/to/leafname/or/leafname_merge -c path/to/clingo/or/$(which clingo)(with the conda installation)
Parameters
| Parameters | Description | Required |
|---|---|---|
| -m/--matrix | {strains X reads} matrice file. | Yes |
| -f/--file | results file from Howde output. | Yes |
| -le/--length | file with one genome and is length per line. It's the output of ORI.py length or ORI.py merge_length. | Yes |
| -l/--listname | list of the bloom filters names (one per line) in the same order than in the matrix. | Yes |
| -c/--clingo_path | clingo path. With a conda installation this path is in $(which clingo). | Yes |
| -o/--output | output results file. | No. Default: out.txt |
| -t/--threshold | Minimum percent value in the matrix for association between reads and species (between 0 and 100). | No. Default: 50 |
| -n/--nbchoices | Only the nbchoices maximum values of a row are considered. Warning, must be less or equal to the number of species. | No. Default: 12 |
As the results are not very readable (especially in case of merge of close strains), it is possible to have cleaner results:
Get cleaner results !
If the genomes of close strains were not merged during the creation of the index, the list_number_file.txt file doesn't exist, it must be created:
num=0; for i in `cat path/to/leafname`;do echo -e "${num} \t ${i}" >> lnf.txt; let num++; done
ORI.py beautiful_results -f path/to/results/from/ORI -n path/to/lnf.txt/or/list_number_file.txt --pie_chart
Parameters
| Parameters | Description | Required |
|---|---|---|
| -f/--file | results file from ORI. | Yes |
| -n/--number_name_list | file containing correspondance between numbers and genomes. It's the output of ORI.py clean_merge (merge_length.txt). | Yes |
| -o/--output | output file. | No. Default: clean_results.txt |
| --pie_chart | create a pie chart of the results in png format. | No |