Class: Bio::SRA::Tables::SRA

Inherits:
Connection
  • Object
show all
Defined in:
lib/bio/sra/tables.rb

Overview

> pp Bio::SRA::Tables::SRA.column_names [“sra_ID”, “SRR_bamFile”, “SRX_bamFile”, “SRX_fastqFTP”, “run_ID”, “run_alias”, “run_accession”, “run_date”, “updated_date”, “spots”, “bases”, “run_center”, “experiment_name”, “run_url_link”, “run_entrez_link”, “run_attribute”, “experiment_ID”, “experiment_alias”, “experiment_accession”, “experiment_title”, “study_name”, “sample_name”, “design_description”, “library_name”, “library_strategy”, “library_source”, “library_selection”, “library_layout”, “library_construction_protocol”, “adapter_spec”, “read_spec”, “platform”, “instrument_model”, “instrument_name”, “platform_parameters”, “sequence_space”, “base_caller”, “quality_scorer”, “number_of_levels”, “multiplier”, “qtype”, “experiment_url_link”, “experiment_entrez_link”, “experiment_attribute”, “sample_ID”, “sample_alias”, “sample_accession”, “taxon_id”, “common_name”, “anonymized_name”, “individual_name”, “description”, “sample_url_link”, “sample_entrez_link”, “sample_attribute”, “study_ID”, “study_alias”, “study_accession”, “study_title”, “study_type”, “study_abstract”, “center_project_name”, “study_description”, “study_url_link”, “study_entrez_link”, “study_attribute”, “related_studies”, “primary_study”, “submission_ID”, “submission_accession”, “submission_comment”, “submission_center”, “submission_lab”, “submission_date”]

Instance Method Summary collapse

Methods inherited from Connection

connect

Instance Method Details

#download_url(options = {}) ⇒ Object

Return the URL where this SRA entry can be downloaded

  sraFileDir <- paste("ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/",
sraType, "/", substring(sra_acc$experiment[i], 1,
    3), "/", substring(sra_acc$experiment[i], 1,
    6), "/", sra_acc$experiment[i], "/", sra_acc$run[i],
"/", sep = "")


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# File 'lib/bio/sra/tables.rb', line 111

def download_url(options = {})
  Bio::SRA::Accession.run_download_url(run_accession, options)
end

#study_download_urls(options = {}) ⇒ Object

URLs of all the runs in this project



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# File 'lib/bio/sra/tables.rb', line 99

def study_download_urls(options = {})
  SRA.where(:study_accession => study_accession).all.collect do |run|
    run.download_url(options)
  end
end