unipept-cli - 4.0.1

For version 4.0, the CLI was reimplemented in node. This should make it easier to install for users and easier to maintain for developers.

All commands use the same syntax, so switching shouldn't be a big problem. For a detailed list of changes, see #172

- TypeScript
Published by bmesuere over 1 year ago

unipept-cli - 3.1.0

This release adds support for the new unipept protinfo command. More information can be found here: https://unipept.ugent.be/clidocs/protinfo.

- TypeScript
Published by bmesuere almost 3 years ago

unipept-cli - 3.0.2

• [Fixed] an issue with the uniprot command due to a change with the UniProtKB website

- TypeScript
Published by bmesuere almost 4 years ago

unipept-cli - 3.0.1

• [Added] psych as an explicit dependency, hopefully fixing #120

- TypeScript
Published by bmesuere about 4 years ago

unipept-cli - 3.0.0

This release switches to the Unipept API v2. There are only minimal changes, but scripts using the output of this tool might break (which is why we bumped the major version number).

More specifically, when requesting the full lineages there are some changes to the ranks that are returned: strain was added and some uncommon ranks such as parvorder were removed. The exact details can be found in this pull request: https://github.com/unipept/unipept/pull/1409

- TypeScript
Published by bmesuere about 4 years ago

unipept-cli - 2.2.2

• [Updated] dependencies
• [Improved] explicit support ruby 3.0 and 3.1
• [Removed] support for ruby 2.5 and 2.6

- TypeScript
Published by bmesuere about 4 years ago

unipept-cli - 2.2.1

• [Fixed] a small bug related to the batch size

- TypeScript
Published by bmesuere about 5 years ago

unipept-cli - 2.2.0

• Add the taxa2tree command to generate a hierarchical json of the taxonomy. The command can also return an HTML view that shows a visualisation.

- TypeScript
Published by bmesuere about 5 years ago

unipept-cli - 2.1.1

• Follow redirects for requests

- TypeScript
Published by bmesuere about 5 years ago

unipept-cli - 2.1.0

Added pept2interpro, updated dependencies and fixed some bug where not all functional annotations were returned (#63).

- TypeScript
Published by bmesuere over 6 years ago

unipept-cli - 2.0.0

Added the unipept pept2ec, unipept pept2go, unipept pept2funct, and unipept peptinfo commands which return additional functional information about the queried peptide.

- TypeScript
Published by bmesuere almost 7 years ago

unipept-cli -

• update cri
• fix travis tests

- TypeScript
Published by bmesuere over 7 years ago

unipept-cli - v1.4.0

• fix uniprot command
• update gems

- TypeScript
Published by bmesuere over 7 years ago

unipept-cli -

• Add a --no-header flag to suppress the output of the header line in the csv output format
• Only add the required output fields when the input is in a fasta-like format
• Don't list blast as an available output format

- TypeScript
Published by bmesuere over 9 years ago

unipept-cli -

• Add the --meganize flag to the unipept pept2prot command, to generate MEGAN-compatible BlastTab-like output

- TypeScript
Published by bmesuere over 9 years ago

unipept-cli -

• add support for ruby 2.4
• update all dependencies

- TypeScript
Published by bmesuere over 9 years ago

unipept-cli -

• Only trap signals that are available
• Drop support for Ruby 1.9

- TypeScript
Published by bmesuere over 9 years ago

unipept-cli - v1.1.1

• Fix a bug where no output was generated in a specific case: https://github.com/unipept/unipept-cli/issues/1

- TypeScript
Published by bmesuere almost 10 years ago

unipept-cli - v1.1.0

• prot2pept now also splits on *

- TypeScript
Published by bmesuere over 10 years ago

unipept-cli - v1.0.1

• Add links to the documentation at http://unipept.ugent.be/clidocs
• Fix an issue where peptfilter crashed when it was called with arguments

- TypeScript
Published by bmesuere almost 11 years ago

unipept-cli - v1.0.0

:tada: version one point oh :tada: - Tweak documentation

- TypeScript
Published by bmesuere almost 11 years ago

unipept-cli - v0.10.0

• Failed requests are now retried 10 times, before failing definitively :tada:
• The host is now set to api.unipept.ugent.be by default
• Fix an issues where name fields were not returned when wildcards in the select option

- TypeScript
Published by bmesuere almost 11 years ago

unipept-cli - v0.9.0

• improve the performance of writing output
• fix a bug where the fasta headers were only included in the csv output and not in the xml and json output
• fix a bug where the xml and json output was invalid if the the input spanned multiple batches

- TypeScript
Published by bmesuere almost 11 years ago

unipept-cli - v0.8.0

• 100% test coverage :tada:
• some major refactoring and improved code style
• remove command aliases
• remove --xml download options
• fixes help output for the uniprot, peptfilter and prot2pept commands

- TypeScript
Published by bmesuere almost 11 years ago

unipept-cli - v0.7.1

• fix broken -all option

- TypeScript
Published by bmesuere about 11 years ago

unipept-cli - v0.7.0

• :warning: Breaking change: renamed a few options for consistency across commands:
  • unipept
  • renamed the extra option to all
  • peptfilter
  • removed the shorthand for minlen and maxlen
  • changed the shorthand for lacks from -a to -l
• Display help output when the unipept command is called without subcommand
• Make help more helpful

- TypeScript
Published by bmesuere about 11 years ago

unipept-cli - v0.6.4

• Use "Unipept CLI - unipept $version" as user agent
• Better logging of failed requests

- TypeScript
Published by bmesuere about 11 years ago

unipept-cli - v0.6.2

• Add more output formats to the uniprot command: fasta, txt, xml, rdf, gff
• Require cri 2.7 for better help formatting

- TypeScript
Published by bmesuere about 11 years ago

unipept-cli - v0.6.1

• Fixed an issue with the mapping of results to the original fasta headers
• Fixed an issue where results were incomplete from the moment there was a failed request
• Fixed a memory leak related to failed requests

- TypeScript
Published by bmesuere about 11 years ago