apollo.io package

Module contents

Contains possible interactions with the Apollo IO Module

class apollo.io.IOClient(webapolloinstance, **requestArgs)

Bases: apollo.client.Client

CLIENT_BASE = '/IOService/'
download(uuid, output_format='gzip')

Download pre-prepared data by UUID

Parameters:
  • uuid (str) – Data UUID
  • output_format (str) – Output format of the data, either “gzip” or “text”
Return type:

str
Returns:

The downloaded content
write_downloadable(organism, export_type='FASTA', seq_type='peptide', export_format='text', export_gff3_fasta=False, sequences=[], region=None)

Prepare a download for an organism

Parameters:
  • organism (str) – organism common name
  • sequences (str) – Names of references sequences to add (default is all)
  • export_type (str) – Export type. Choices: FASTA, GFF3, VCF
  • seq_type (str) – Export selection. Choices: peptide, cds, cdna, genomic
  • export_format (str) – Export format, either gzip or text
  • export_gff3_fasta (bool) – Export reference sequence when exporting GFF3 annotations.
  • region (str) – Region to export in form sequence:min..max e.g., chr3:1001..1034
Return type:

dict
Returns:

a dictionary containing download information
write_text(organism, export_type='FASTA', seq_type='peptide', export_format='text', export_gff3_fasta=False, sequences=[], region=None)

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

Parameters:
  • organism (str) – organism common name
  • sequences (str) – Names of references sequences to add (default is all)
  • export_type (str) – Export type. Choices: FASTA, GFF3, VCF
  • seq_type (str) – Export selection. Choices: peptide, cds, cdna, genomic
  • export_format (str) – Export format, either gzip or text
  • export_gff3_fasta (bool) – Export reference sequence when exporting GFF3 annotations.
  • region (str) – Region to export in form sequence:min..max e.g., chr3:1001..1034
Return type:

str
Returns:

the exported data