bioutils

Commit Graph

Author	SHA1	Message	Date
Damien Goutte-Gattat	0e801b94ea	Switch to Black-enforced code style.	2 months ago
Damien Goutte-Gattat	fa20c968af	Switch back to the original click-shell. Development of click-shell has resumed, so we no longer have to rely on our own fork.	1 year ago
Damien Goutte-Gattat	4b3cffa39c	Replace click_shell by incenp.click_shell.	1 year ago
Damien Goutte-Gattat	b9723dcd10	Prepare the 0.2.0 release.	2 years ago
Damien Goutte-Gattat	671486d80c	Add more documentation. Start properly documenting the project in a Sphinx-based manual.	2 years ago
Damien Goutte-Gattat	df47a1ed6c	Allow seqtool to access user-configured databases. Make seqtool use the default DatabaseProvider object, so that it can fetch sequences from any database listed in databases.ini.	2 years ago
Damien Goutte-Gattat	b3d14b925f	Remove the seqvault.rc configuration file. Make the seqvault program use the same configuration file as the default DatabaseProvider object. Also remove the possibility to specify server settings on the command line. This effectively makes the presence of a configuration file mandatory.	2 years ago
Damien Goutte-Gattat	5f5f96b6ad	Change option for database name in databases.ini. In the configuration file for databases, change the name of the option indicating the database name from `name' to `database', for clarity.	2 years ago
Damien Goutte-Gattat	d18fa3ea7d	Change location of seqvault's configuration file. Make seqvault look for a seqvault.rc file in the $XDG_CONFIG_HOME/bioutils directory.	2 years ago
Damien Goutte-Gattat	73d28dc432	Add more documentation.	2 years ago
Damien Goutte-Gattat	3fab6608c0	Improve documentation of the USA module.	2 years ago
Damien Goutte-Gattat	c9e45ce936	Remove unneeded import. The usa module is no longer coupled to the databases module.	2 years ago
Damien Goutte-Gattat	efc07ed7ca	Remove query methods from the DatabaseProvider class. With the new dict-like interface, that class is no longer supposed to be used to query the databases directly. Client code should instead get the database adapter from the dictionary and then use the adapter to perfor any query.	2 years ago
Damien Goutte-Gattat	a82269f98c	Use a dict-like interface for the DatabaseProvider. Make the DatabaseProvider object use a dict-like interface to check if a database name exists and to get a database adapter. This allows the USA code to accept a mere dictionary (with database names as keys and database adapters as values) instead of a DatabaseProvider object. Rename the `db_provider' argument to `databases' to reflect that change.	2 years ago
Damien Goutte-Gattat	63a14f1d85	Do not use a global DatabaseProvider object. Make the read_usa and parse_usa functions accept an optional db_provider argument instead of relying on a module-level global DatabaseProvider object.	2 years ago
Damien Goutte-Gattat	4230b44a1f	Fix creation of an unprefixed database. A typo (missing closing parenthesis) prevented the creation of a new subdatabase on a BioSQL server without support for prefixed databases.	2 years ago
Damien Goutte-Gattat	d08bde1e5a	seqvault: Add support for SQLite databases. Add the (unreleased by upstream) BioSQL schema for SQLite3. Fix detection of the 'prefix' column.	2 years ago
Damien Goutte-Gattat	b64f943c77	seqvault: Fix creation of a new database. Add a missing call to commit() to make sure the new database is indeed created.	2 years ago
Damien Goutte-Gattat	3437bc4031	Add the expasy and entrez database sources. Add adapters to allow fetching sequences from the NCBI servers and from ExPASy.	2 years ago
Damien Goutte-Gattat	9e3e02afcd	Support SQLite-backed BioSQL databases. Add support for sqlite3 driver for BioSQL databases. Unfortunately this involves having to add an explicit 'ESCAPE' clause to all queries as sqlite3 does not define any escape character by default.	2 years ago
Damien Goutte-Gattat	30da42775b	Use a single adapter for BioSQL-based databases. Do not use one adapter for BioSQL subdatabases and another one for BioSQL "entire" databases. Merge the two into a single adapter and adjust the SQL queries when needed.	2 years ago
Damien Goutte-Gattat	5cfd8b0b6f	Support wildcards when querying a BioSQL database. Implement support for '*' and '?' wildcards in database-backed USAs.	2 years ago
Damien Goutte-Gattat	f7735db4eb	Allow access to a specific subdatabase. A BioSQL server contains subdatabases. This patch allows to define a database source corresponding to a single subdatabase, while still allowing to define a source corresponding to the entire server (spanning all subdatabases).	2 years ago
Damien Goutte-Gattat	7bf4106794	Change the DatabaseProvider interface. Do not use a single method for all kind of queries. Instead, use 3 distinct methods for fetching records based on a identifier, fetching records based on a field query, and fetching all records.	2 years ago
Damien Goutte-Gattat	439255721c	Rough implementation of the database access layer. Start implementing fetching records from database-backed USAs. Only BioSQL-based databases are supported for now.	2 years ago
Damien Goutte-Gattat	c1a8553eef	Prepare 0.1.2 release.	2 years ago
Damien Goutte-Gattat	31b216528a	Fix Click interface for the blast tool. Add the missing pass_context decorator to the definition of the blast tool.	2 years ago
Damien Goutte-Gattat	e89320c0a2	Prepare 0.1.1 release. Present the USA module in the README; bump version number and add the NEWS file.	2 years ago
Damien Goutte-Gattat	f253447794	Compile search patterns in database-based USAs. When creating a database-based USAs, compile the search pattern given (if any). This will be used when fetching records from a database-based USA is actually implemented.	2 years ago
Damien Goutte-Gattat	ae29033b6b	Only allow valid search fields. When parsing a file-based or database-based USA, check that the search field, if any, is one of the fields allowed by the USA specification.	2 years ago
Damien Goutte-Gattat	d0f5ca6339	Implement per-field search in USAs. When reading a file-based USA, allow to filter sequences based on explicitly specified fields.	2 years ago
Damien Goutte-Gattat	c36e3f352b	Match identifier against unversioned accession number. If a record’s accession number contains a version number, ignore it when matching against an identifier.	2 years ago
Damien Goutte-Gattat	b43e77c717	Use both name and id when matching a record against an identifier. The USA specification says that unless a ID or ACC field is explicitly used, an identifier in a USA should match against any of the two fields.	2 years ago
Damien Goutte-Gattat	660ea77f3c	Support wildcard ID lookups. Add support for USAs with wildcard ID specifiers.	2 years ago
Damien Goutte-Gattat	8a6448ad2f	Support reading from program-based USAs. Implement fetching sequences from a ProgramUSA object.	2 years ago
Damien Goutte-Gattat	c849b899e4	Reuse first record's details when catenating sequences. When catenating several sequences into one, default to copying the details and annotations from the first sequence.	2 years ago
Damien Goutte-Gattat	a87abf8e62	Add dependencies in setup.py. Add Biopython as a required dependency, and reportlab as an optional dependency. Do not require reportlab to launch the seqtool program.	2 years ago
Damien Goutte-Gattat	d26b0741c3	Fix invocation of the plasmm command. The plasmm command expects an array of USA specs.	2 years ago
Damien Goutte-Gattat	c146e376f0	Autodetect format for file-based USAs. When parsing a file-based USA, try to guess the format from the extension if no explicit format is specified.	2 years ago
Damien Goutte-Gattat	209f190b70	Add the newdb command. Add a command to create a new biodatabase.	2 years ago
Damien Goutte-Gattat	b01e79ccdb	Fix incorrect use of is_prefixed(). One call to is_prefixed was still using the temporary name of is_prefixed_biosql().	2 years ago
Damien Goutte-Gattat	5d679630d2	Support edit records in unprefixed databases. The edit command was relying on the existence of database prefixes. Make it work also in unprefixed databases.	2 years ago
Damien Goutte-Gattat	3712e13548	Add support for non-modified BioSQL servers. Make the classes in vault.py support BioSQL servers that use the unmodified BioSQL schema.	2 years ago
Damien Goutte-Gattat	d5c5b4e4c7	Add the ipython command to seqvault. Add a command to start a IPython shell. This is mainly intended for development and debugging, but could be useful for an end-user as well.	2 years ago
Damien Goutte-Gattat	7a6c2657c4	Convert cc3d.py to Click. Use a Click-based interface for cc3d instead of using argparse.	2 years ago
Damien Goutte-Gattat	d508e69d7f	Allow missing default configuration file. It should not be an error if the default configuration does not exist. Only if a configuration file has been explicitly specified on the command line should we check that it does exist.	2 years ago
Damien Goutte-Gattat	71342729b9	Add some error handling. Catch some error situations in SeqVault.	2 years ago
Damien Goutte-Gattat	ab6e617215	Rework the seqvault command. Move the seqvault command to a separate Click-based module.	2 years ago
Damien Goutte-Gattat	1b4084fd91	Reorganize the seq utilities. Regroup all command-line tools into a single Click-based master tool.	2 years ago
Damien Goutte-Gattat	92bd0186ab	Add draft version of the vault command. Add a command acting as a user-facing interface to a BioSQL database.	2 years ago

1 2

70 Commits (master)