ena-upload-cli 0.3.1

Command Line Interface to upload data to the European Nucleotide Archive

ENA upload tool

About

The program submits experimental data and respective metadata to the European Nucleotide Archive (ENA). The metadata should be provided in separate tables corresponding to the following ENA objects:

• STUDY
• SAMPLE
• EXPERIMENT
• RUN

The program to perform the following actions:

• add: add an object to the archive
• modify: modify an object in the archive
• cancel: cancel a private object and its dependent objects (under development)
• release: release a private object immediately to the public (under development)

After a successful submission, new tsv tables will be generated with the ENA accession numbers filled in along with a submission receipt.

Tool dependencies

• python 3.5+ including following packages:
  • Genshi
  • lxml
  • pandas
  • requests

Installation

pip install ena-upload-cli

Usage

Minimal:  ena-upoad-cli --action {add,modify,cancel,release} --center CENTER_NAME  --secret SECRET

All supported arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  --action {add,modify,cancel,release}
                         add: add an object to the archive
                         modify: modify an object in the archive
                         cancel: cancel a private object and its dependent objects
                         release: release a private object immediately to public
  --study STUDY         table of STUDY object
  --sample SAMPLE       table of SAMPLE object
  --experiment EXPERIMENT
                        table of EXPERIMENT object
  --run RUN             table of RUN object
  --data [FILE [FILE ...]]
                        data for submission
  --center CENTER_NAME  specific to your Webin account
  --tool TOOL_NAME      Specify the name of the tool this submission is done with. Default: ena-upload-cli
  --tool_version TOOL_VERSION
                        Specify the version of the tool this submission is done with. Default: current version of tool
  --secret SECRET       .secret file containing the password of your Webin account
  -d, --dev             Flag to use the dev/sandbox endpoint of ENA.
  --vir                 Flag to use the viral sample template.

Mandatory arguments: --action, --center and --secret.

ENA Webin

A Webin can be made here if you don't have one already. The --webin_id parameter makes use of the full username looking like: Webin-XXXXX. Visit Webin online to check on your submissions or dev Webin to check on test submissions.

The .secret.yml file

To avoid exposing your credentials through the terminal history, it is recommended to make use of a .secret.yml file, containing your password and username keywords. An example is given in the root of this directory.

Dev instance

By default the submission will be done using following url to ENA: https://www.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA

Use the --dev flag if you want to do a test submission using the tool by the sandbox dev instance of ENA: https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA. A TEST submission will be discarded within 24 hours.

Supported columns for viral sample submissions

Viral samples are validated by ENA using the ENA virus pathogen checklist. The columns supported in the sample tsv table used by this tool are:

Column name	ENA field name	Field format	Cardinality
alias	alias	free text	mandatory
status			auto_filled
accession	accession		auto_filled
title	TITLE	free text	mandatory
scientific_name	SCIENTIFIC_NAME	free text	mandatory
taxon_id	TAXON_ID		auto_filled
sample_description	DESCRIPTION	free text	mandatory
submission_date			auto_filled
geographic_location	geographic location (country and/or sea)	text choice	mandatory
host_common_name	host common name	free text	mandatory
host_subject_id	host subject id	free text	mandatory
host_health_state	host health state	text choice	mandatory
host_sex	host sex	text choice	mandatory
host_scientific_name	host scientific name	free text	mandatory
collector_name	collector name	free text	mandatory
collecting_institution	collecting institution	free text	mandatory
isolate	isolate	free text	mandatory
collection_date	collection date	restricted text	recommended
geographic_location_latitude	geographic location (latitude)	restricted text	recommended
geographic_location_longitude	geographic location (longitude)	restricted text	recommended
geographic_location_region	geographic location (region and locality)	free text	recommended
sample_capture_status	sample capture status	text choice	recommended
host_disease_outcome	host disease outcome	text choice	recommended
host_age	host age	restricted text	recommended
virus_identifier	virus identifier	free text	recommended
receipt_date	receipt date	restricted text	recommended
definition_for_seropositive_sample	definition for seropositive sample	free text	recommended
serotype	serotype (required for a seropositive sample)	free text	recommended
host_habitat	host habitat	text choice	recommended
isolation_source_host_associated	isolation source host-associated	free text	recommended
host_behaviour	host behaviour	text choice	recommended
isolation_source_non_host_associated	isolation source non-host-associated	free text	recommended
subject_exposure	subject exposure	free text	optional
subject_exposure_duration	subject exposure duration	free text	optional
type_exposure	type exposure	free text	optional
personal_protective_equipment	personal protective equipment	free text	optional
hospitalisation	hospitalisation	text choice	optional
illness_duration	illness duration	free text	optional
illness_symptoms	illness symptoms	free text	optional
sample_storage_conditions	sample storage conditions	free text	optional
strain	strain	free text	optional
host_description	host description	free text	optional
gravidity	gravidity	free text	optional

Please use the ENA virus pathogen checklist on the website of ENA to know which values are allowed/possible in the restricted text and text choice fields.

The data files

Supported data

• Read data
• Genome Assembly
• Transcriptome Assembly
• Template Sequence
• Other Analyses

Most files uploaded to the ENA FTP server need to be compressed.

More information on how ENA wants to receive the files can be found here.

Tool overview

inputs:

• metadata tables
  • examples in example_table
  • Please define actions in status column e.g. add, modify, cancel, release
  • to perform bulk submission of all objects, the aliases ids in different ENA objects should be in the association where alias ids in experiment object link all objects together
• experimental data
  • examples in example_data

outputs:

• In the same directory of inputs
• metadata tables with updated info in status and other relevant columns, e.g:
  • updated status: added, modified, canceled, released
  • accession ids
  • submission date

Test the tool

test command: add metadata and sequence data

ena_upload --action add --center 'your_center_name' --study example_tables/ENA_template_studies.tsv --sample example_tables/ENA_template_samples.tsv --experiment example_tables/ENA_template_experiments.tsv --run example_tables/ENA_template_runs.tsv --data example_data/*gz --dev --secret .secret.yml

test command: modify metadata

ena_upload --action modify --center 'your_center_name' --study example_tables/ENA_template_studies-2020-05-01T1421.tsv --dev --secret .secret.yml

test command for viral data

ena_upload --action add --center 'your_center_name' --study example_tables/ENA_template_studies.tsv --sample example_tables/ENA_template_samples_vir.tsv --experiment example_tables/ENA_template_experiments.tsv --run example_tables/ENA_template_runs.tsv --data example_data/*gz --dev --vir --secret .secret.yml