Transcriptome Index

class pyrefinebio.TranscriptomeIndex(id=None, assembly_name=None, organism_name=None, database_name=None, release_version=None, index_type=None, salmon_version=None, download_url=None, result_id=None, last_modified=None)

Transcriptome Index.

get a TranscriptomeIndex by id

>>> import pyrefinebio
>>> id = 1
>>> t_index = pyrefinebio.TranscriptomeIndex.get(id)

Retrieve a list of TranscriptomeIndex based on filters

>>> import pyrefinebio
>>> t_indecies = pyrefinebio.TranscriptomeIndex.search(organism_name="GORILLA")
classmethod get(id)

Retrieve a TranscriptomeIndex based on id

Returns:

TranscriptomeIndex

Parameters:

id (int) – the id for the TranscriptomeIndex you want to get

classmethod search(**kwargs)

Retrieve a list of TranscriptomeIndex based on various filters

Returns:

list of TranscriptomeIndex

Keyword Arguments:

  • salmon_version (str) – filter based on the TranscriptomeIndex’s salmon version eg. salmon 0.13.1

  • index_type (str) – TRANSCRIPTOME_LONG or TRANSCRIPTOME_SHORT. If the average read length of the RNA-Seq sample you want to process is greater than 75 base pairs, use TRANSCRIPTOME_LONG otherwise use TRANSCRIPTOME_SHORT

  • ordering (str) – which field to use when ordering the results.

  • limit (int) – number of results to return per page.

  • offset (int) – the initial index from which to return the results.

  • organism__name (str) – filter based on the name of the Organism associated with the TranscriptomeIndex

  • length (str) – short hand for index_type eg. short or long see index_type for more information