create_matrix - calculate the genome abundance similarity
matrix
create_matrix [options] NAMES
Calculate the similarity matrix.
First, a set of reads is simulated for every reference genome
using a read simulator from core/tools.py specified via -s. Second,
the simulated reads of each species are mapped against all reference genomes
using the mapper specified with -m. Third, the resulting SAM-files
are analyzed to calculate the similarity matrix. The similarity matrix is
stored as a numpy file (-o).
- NAMES
- Filename of the names file; the plain text names file should contain one
name per line. The name is used as identifier in the whole algorithm.
- -h, --help
- show this help message and exit
- -s SIMULATOR,
--simulator=SIMULATOR
- Identifier of read simulator defined in core/tools.py [default: none]
- -r REF,
--reference=REF
- Reference sequence file pattern for the read simulator. Placeholder for
the name is "%s". [default: ./ref/%s.fasta]
- -m MAPPER,
--mapper=MAPPER
- Identifier of mapper defined in core/tools.py [default: none]
- -i INDEX,
--index=INDEX
- Reference index files for the read mapper. Placeholder for the name is
"%s". [default: ./ref/%s.fasta]
- -t TEMP,
--temp=TEMP
- Directory to store temporary simulated datasets and SAM files. [default:
./temp]
- -o OUT,
--output=OUT
- Output similarity matrix file. [default: ./similarity_matrix.npy]