enaBrowserTools-v1.5.2

Resolves failures using enaDataGet due to ENA Portal API anon auth removal.
Fixed obsolete anon authentication for calling the ENA Portal API.

enaBrowserTools-v1.5.1

Added expanded flag to expand CON records when retrieving the embl format for sequences/assemblies
Fixed a problem with Python3 file writes
Added information on fixing Python3 certificate issue on Mac

enaBrowserTools-v1.5

Following updates/improvments made:

• Improved checks for Aspera files and binary
• Handle known Python 3 Mac installation problem impacting HTTPS URLs
• Don't re-download run/analysis file if exists (with MD5 check)
• Replace (rather than append to) sequence files if they exist
• Download WGS set if WGS-only assembly or assembly contains WGS scaffolds (even without WGS flag)
• Added flag to extract WGS scaffolds from WGS file into wgs_scaffolds file
• Added some progress information to enaDataGet assembly fetch

enaBrowserTools-v1.4.1

Assembly fix for python3 scripts
LICENCE file and text added

enaBrowserTools-v1.4

Changes in release v1.4

This release has three main changes:

1. Change to aspera flags/options and how to define location of aspera settings file
2. Default to using FTP if aspera settings or licence file cannot be found/read
3. Improve the default format option for read data

Aspera setting file and flag/option changes

There are two command line flags/options available if you wish to use aspera for download. These are:

1. -a (or --aspera): use this flag if you'd like to download with aspera.
2. -as (or --aspera-settings): use this option if you'd like to specify the location of your aspera settings file. If you use this option, you don't need to use the --aspera flag.

See the readme file for more details.

Default format option for read data

The default format option (that is, when -f/--format command line option is not used), the scripts will look for available files in the following order: submitted, sra, fastq.

A word of advice for read formats:

• submitted: only read data submitted to ENA have files available as submitted by the user.
• sra: this is the NCBI SRA format, and is the format in which all NCBI/DDBJ data is mirrored to ENA.
• fastq: not all submitted format files can be converted to FASTQ

enaBrowserTools-v1.3.2

This release fixes aspera errors in the python3 scripts. It also changes the aspera command to use the new port, see http://www.ebi.ac.uk/about/news/service-news/update-aspera-server

enaBrowserTools-v1.3.1

Small updates/fixes as reported by users:

• Don't download a file if it already exists in the local target directory
• Move aspera settings to external file that is passed in using the --aspera option
• Fix for non-versioned suppressed WGS set fetch
• Fix for withdrawn sequences

enaBrowserTools-v1.3

New to this release:

• NCBI tax ID support added to enaGroupGet for WGS, assembly and sequence data

Updates/fixes in the release:

• symlinked bash files now correctly find python script
• python -> python3 in python3 bash scripts (may cause problems if only python3 is installed and under 'python' command)
• sub-task scripts (and main methods) have been removed; now just have enaDataGet and enaGroupGet
• error messages now written to stderr; but informational messages still printed to stdout
• python exception messages now exposed from file downloading as we couldn't reproduce the problem users were reporting with R2 fastq files
• if no files of requested format for a run, a message is displayed and empty run directory deleted

enaBrowserTools-v1.2

Aspera support added for downloading read and analysis data.
Universal MD5 calculation to avoid different commands (and output) for different platforms

enaBrowserTools-v1.1

Expanded WGS support so that versioned and unversioned prefix and master accessions can be used to download a WGS set. For example, to download the set AAAK03, use any of:
AAAK03 (previously supported)
AAAK03000000
AAAK
AAAK00000000

The latter two will always fetch the latest version. For earlier (suppressed) versions, the specific version must be requested, e.g. AAAK02

The master format must now be used if the master record is required.