io

This section is auto-generated from the help text for the arrow command io.

download command

Usage:

arrow io download [OPTIONS] UUID

Help

Download pre-prepared data by UUID

Output

The downloaded content

Options:

--output_format TEXT  Output format of the data, either "gzip" or "text"
                      [default: gzip]

-h, --help            Show this message and exit.

write_downloadable command

Usage:

arrow io write_downloadable [OPTIONS] ORGANISM

Help

Prepare a download for an organism

Output

a dictionary containing download information

Options:

--export_type TEXT    Export type. Choices: FASTA, GFF3, VCF  [default: FASTA]
--seq_type TEXT       Export selection. Choices: peptide, cds, cdna, genomic
                      [default: peptide]

--export_format TEXT  Export format, either gzip or text  [default: text]
--export_gff3_fasta   Export reference sequence when exporting GFF3
                      annotations.

--sequences TEXT      Names of references sequences to add (default is all)
--region TEXT         Region to export in form sequence:min..max e.g.,
                      chr3:1001..1034

-h, --help            Show this message and exit.

write_text command

Usage:

arrow io write_text [OPTIONS] ORGANISM

Help

[DEPRECATED, use write_downloadable] Download or prepare a download for an organism

Output

the exported data

Options:

--export_type TEXT    Export type. Choices: FASTA, GFF3, VCF  [default: FASTA]
--seq_type TEXT       Export selection. Choices: peptide, cds, cdna, genomic
                      [default: peptide]

--export_format TEXT  Export format, either gzip or text  [default: text]
--export_gff3_fasta   Export reference sequence when exporting GFF3
                      annotations.

--sequences TEXT      Names of references sequences to add (default is all)
--region TEXT         Region to export in form sequence:min..max e.g.,
                      chr3:1001..1034

-h, --help            Show this message and exit.