singlem create

DESCRIPTION

Create a SingleM package.

OPTIONS

--input-graftm-package PATH

Input GraftM package underlying the new SingleM package. The GraftM package is usually made with 'graftM create --no_tree --hmm <your.hmm>' where <your.hmm> is the one provided to 'singlem seqs'.

--input-taxonomy PATH

Input taxonomy file in GreenGenes format (2 column tab separated, ID then taxonomy with taxonomy separated by ';' or '; '.

--output-singlem-package PATH

Output package path

--hmm-position INTEGER

Position in the GraftM alignment HMM where the SingleM window starts. To choose the best position, use 'singlem seqs'. Note that this position (both the one output by 'seqs' and the one specified here) is a 1-based index, but this positions stored within the SingleM package as a 0-based index.

--window-size INTEGER

Length of NUCLEOTIDE residues in the window, counting only those that match the HMM [default: 60]

--target-domains TARGET_DOMAINS [TARGET_DOMAINS ...]

Input domains targeted by this package e.g. 'Archaea', 'Bacteria', 'Eukaryota' or 'Viruses'. Input with multiple domains must be space separated.

--gene-description STRING

Input free form text description of this marker package, for use with 'singlem metapackage --describe'.

--force

Overwrite output path if it already exists [default: false]

OTHER GENERAL OPTIONS

--debug

output debug information

--version

output version information and quit

--quiet

only output errors

--full-help

print longer help message

--full-help-roff

print longer help message in ROFF (manpage) format

AUTHORS

Ben J. Woodcroft, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology
Samuel Aroney, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology
Raphael Eisenhofer, Centre for Evolutionary Hologenomics, University of Copenhagen, Denmark
Rossen Zhao, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology