Man page - create_matrix(1)

Packages contains this manual

Package:  gasic
apt-get install gasic

Manuals in package:
• correct_abundances(1)
• quality_check(1)
• create_matrix(1)
• run_mappers(1)
Documentations in package:
• gasic

Manual

CREATE_MATRIX

NAME
SYNOPSIS
DESCRIPTION
OPTIONS

---

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]

---