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create_matrix - calculate the genome abundance similarity matrix

CREATE_MATRIX(1) User Commands CREATE_MATRIX(1)

NAME

create_matrix - calculate the genome abundance similarity matrix

SYNOPSIS

create_matrix [ options] NAMES

DESCRIPTION

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).

OPTIONS

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]
February 2014 create_matrix SVNr18