kingfisher annotate

DESCRIPTION

Annotate runs by their metadata e.g. number of sequenced bases, BioSample attributes, etc.

OPTIONS

-r, --run-identifiers RUN_IDENTIFIERS [RUN_IDENTIFIERS ...]

Run number to download/extract e.g. ERR1739691

--run-identifiers-list, --run-accession-list, --run-identifiers-list RUN_IDENTIFIERS_LIST

Text file containing a newline-separated list of run identifiers i.e. a 1 column CSV file.

-p, --bioprojects BIOPROJECTS [BIOPROJECTS ...]

BioProject IDs number(s) to download/extract from e.g. PRJNA621514 or SRP260223

-o, --output-file OUTPUT_FILE

Output file to write to [default: stdout]

-f, --output-format {human,csv,tsv,json,feather,parquet}

Output format [default human]

-a, --all-columns

Print all metadata columns [default: Print only a few select ones]

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

AUTHOR

Ben J. Woodcroft, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology <benjwoodcroft near gmail.com>

EXAMPLES

Annotate the metadata of a run

$ kingfisher annotate -r ERR1739691

Output metadata of all runs in a BioProject to a CSV file

$ kingfisher annotate --bioprojects PRJNA177893 -o PRJNA177893.csv -f csv

Output the full set of metadata from a run

$ kingfisher annotate -r ERR1739691 -a