source: parsers

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(edit) @305   10 years jjbot Many changes in the different parsers. basicparses can now be used as …
(edit) @302   10 years jjbot Changed class name from FieldParser? to ArrayParser?, now base names on …
(edit) @301   10 years jjbot First version of new basicparsers: this module should provide simple …
(edit) @297   10 years jjbot First versions of gal and arrayparsers.
(edit) @295   10 years jjbot Implemented iterator function in Obo2.py. Can also use slices to get …
(edit) @294   10 years jjbot First version of new obo parser.
(edit) @276   10 years jjbot Parser improvements. Fixed type and set IDs in biomart parser. Added …
(edit) @275   10 years jjbot Bug fixes which caused the type of item_link_props not to be flushed.
(edit) @271   10 years jjbot Commit voor Evert 2
(edit) @253   10 years jjbot First version of ibidasflusher and biomart parser. Updated liner.
(edit) @239   10 years jjbot Bug fixes in transfacgeneparser. Added ontology to …
(edit) @236   10 years jjbot Added more parsing functions to Transfac parser, can now also parse …
(edit) @233   10 years jjbot First version of transfac parser. Minor improvements to msigdb2 parser.
(edit) @232   10 years jjbot Fixed bug in field mapping.
(edit) @230   10 years pvkouteren Bugfixes (mostly regarding calls to the logger)
(edit) @228   10 years jjbot Added flusher for the interpro go terms.
(edit) @227   10 years jjbot Added flush functionality to interpro, fixed a nasty bug with Marc. …
(edit) @225   10 years jjbot Added first version of the interpro flusher and support functions. …
(edit) @224   10 years jjbot First version of the Interpro XML parser. We need this for the work of …
(edit) @221   10 years jjbot Added some logging capabilities. Now using singleton logger to make …
(edit) @216   10 years jjbot Clean-ups
(edit) @215   10 years jjbot Added new parser for msigdb, added type to ibidas ontology to support …
(edit) @214   10 years jjbot Added type information to i2d data. Added direct imports of genenames …
(edit) @207   10 years jjbot First version of the I2D parser.
(edit) @205   10 years pvkouteren source_ids are flushed with the term_child_links
(edit) @196   10 years jjbot Created parser for Uniprot synonym files.
(edit) @194   10 years jjbot Initial upload of splitter.py, a file which splits texts files based …
(edit) @193   10 years jjbot Now contains bogus type_id when flushing to get around the NOT NULL …
(edit) @190   10 years jjbot Added small function which allows you to only include certain records …
(edit) @189   10 years jjbot First upload of the goa and genename parsers.
(edit) @188   10 years jjbot Moved datasetResolver to flush_utils so other classes can use it too.
(edit) @182   10 years jjbot Changed some identifiers in the sql file (added item_id and term_id to …
(edit) @173   10 years jjbot First version of the 2nd refseq parser. This one uses the BioPython?
(edit) @172   10 years jjbot Changed type of set.version to string. Changed obo parser to reflect …
(edit) @169   10 years jjbot Fixed small mistake that caused datasets to not set the type_id when …
(edit) @167   10 years jjbot Fixes to parsers, added small flusher to hapmap parser. Clean-up & …
(edit) @164   10 years jjbot Altered liner to use the python csv module and only use the function …
(edit) @162   10 years jjbot Cleaned and extended some ontologies, added flush code to schuemie …
(edit) @160   10 years jjbot Bug fixes to obo parser: added dataset id to the terms.
(edit) @145   10 years jjbot Very simple kegg parser, only extracts the EC numbers from the ECList file.
(edit) @144   10 years jjbot Small fix to prevent obsolete entries from being flushed into the database.
(edit) @142   10 years jjbot Added item_accession to the database, added unit tests and played …
(edit) @138   10 years marchulsman Many changes
(edit) @136   10 years jjbot Clean svn import to sync all repositories. All minor changes except …
(edit) @122   10 years jjbot Untracked changes of last week.
(edit) @103   10 years jjbot Added unittests for union, join, and stack functions of …
(edit) @99   10 years jjbot Bugfixes (unicode fix). Now flushes RO, SO, GO & PSI-MI.
(edit) @97   10 years jjbot Bug fixes (index errors, caching mistakes), additional unittests. …
(edit) @94   10 years jjbot Bugfixes (cd.set default field value error), appending single item in …
(edit) @89   10 years jjbot Documentation changes, util function to add terms to the db.
(edit) @86   10 years jjbot Clean-ups, documentation, added shortcut for parsing freq files.
(edit) @83   10 years jjbot Added some documentation on where to get the ontology files and …
(edit) @80   10 years jjbot Some changes to parsers to facilitate flushing of the data to the …
(edit) @53   10 years pvkouteren Adjusted RefSeq? parser Fixed issue with Fasta parser
(edit) @52   11 years pvkouteren Adjusted parsers to ParserFactory? / GenericParser? idea. The parsers …
(edit) @41   11 years pvkouteren Modified parsers for prerequisites. Made a start with import order in …
(edit) @40   11 years pvkouteren run_imports contains an example of importing through the Importer …
(edit) @23   11 years jjbot First version of uniprot parser.
(edit) @21   11 years jjbot Minor changes in parse structure.
(edit) @20   11 years jjbot GFF parser to be used with the MacIsaac? dataset.
(edit) @19   11 years jjbot Added comment functionality, now ignores all lines which start with a …
(edit) @17   11 years jjbot Created first version of obo (ontology) parser. Added function to …
(edit) @8   11 years jjbot New parser functionality, now able to parse hapmap freq and ld files …
(edit) @7   11 years jjbot Parser now supports new lines as end-of-record indicator.
(edit) @5   11 years jjbot Added sequence loading to fasta parser.
(add) @4   11 years jjbot Initial import of new code base.
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