Class: Bio::SRA::Tables::SRA
- Inherits:
-
Connection
- Object
- ActiveRecord::Base
- Connection
- Bio::SRA::Tables::SRA
- 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
-
#download_url(options = {}) ⇒ Object
Return the URL where this SRA entry can be downloaded sraFileDir <- paste(“ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/”, sraType, “/”, substring(sra_acc$experiment, 1, 3), “/”, substring(sra_acc$experiment, 1, 6), “/”, sra_acc$experiment, “/”, sra_acc$run, “/”, sep = “”).
-
#study_download_urls(options = {}) ⇒ Object
URLs of all the runs in this project.
Methods inherited from Connection
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( = {}) Bio::SRA::Accession.run_download_url(run_accession, ) 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( = {}) SRA.where(:study_accession => study_accession).all.collect do |run| run.download_url() end end |