README.md

Evaluation framework used for the PPS+ pipeline (author: Ivan)

Method

The evaluation measures are described in sections 4.9 and 4.10 (http://arxiv.org/pdf/1406.7123v1.pdf).

Usage

The master script that performs the default task in the sense of https://github.com/bioboxes/rfc/blob/master/container/binning-evaluation.mkd (version 0.8.0) is: algbioi.eval.default_task_eval_ivan.py

Warning: this is an initial version for testing!!!

Note that all scripts require python 2.7 (including biopython, sqlite3). The evaluation framework is distributed as a python package (algbioi). Individual evaluation scripts are contained in package (algbioi.eval), helper functionality in (algbioi.com). To run the scripts, you need to set the PYTHONPATH variable pointing to the folder that contains the main (algbioi) package.

You can also run any of the following script with -h to get all available options.

Precision and Recall including correction

Standard use:

python accuracy.py -f FASTA_CONTIG_FILE -p TAXONOMIC_ASSIGNMENTS -t TRUE_TAXONOMIC_LABELS \
-d NCBI_TAXONOMY_IN_SQLITE3_FORMAT -c 0.01 -b 0.01 -o

Using the correction option:

python accuracy.py -f FASTA_CONTIG_FILE -p TAXONOMIC_ASSIGNMENTS -t TRUE_TAXONOMIC_LABELS \
-d NCBI_TAXONOMY_IN_SQLITE3_FORMAT -c 0.01 -b 0.01 -o -m 0.9

Scaffold-contig consistency

python consistency.py -f FASTA_CONTIG_FILE -p TAXONOMIC_ASSIGNMENTS -m SCAFFOLD_CONTIG_MAPPING \
-d NCBI_TAXONOMY_IN_SQLITE3_FORMAT -a

Confusion matrices

python confusion_matrix.py -f FASTA_CONTIG_FILE -p TAXONOMIC_ASSIGNMENTS -t TRUE_TAXONOMIC_LABELS \
-d NCBI_TAXONOMY_IN_SQLITE3_FORMAT -o ./prefix_