[2.0.0.post1] - 2019-01-25

Added

• bioext module for biological file extension methods.
  • UCSCbed class to read files in UCSC bed format.
• web module for web-service related methods.
  • UCSC DAS server related methods.
• query module for query and database management.
  • Implemented oligo database class that asserts it when reading it.
• stats module for statistics-related methods.
• fprode_mkdb script: re-format a database to be compatible with FISH-ProDe.
  • List UCSC available reference genomes with --list-refGenomes.
  • .config file generated using the configparser package.
• fprode_dbchk: checks database integrity.
• Parallelization to probe set query script. (only local)

Changed

• Renamed package to ifpd.
• Moved interface documents to separate sub-folder.
• Each database is structured as follows:
  • One file per chromosome, with the name being the same as the chromosome. One row per oligo and two columns: start and end position, as per the UCSC bed format standard. Also, a third (optional) column can be present, with the sequence of the oligo.
  • One .config file with the database details.
• Database query now split in two scripts (fprode_dbquery_probe and fprode_dbquery_probeSet), for single-probe and probe-set design.
  • Query-related methods moved to the query sub-module.
  • Query ID now handled server-side, for easier standalone script execution.
  • Region of interest now passed as chrN:XXX,YYY, for convenience.
  • Query name and description now handled only server-side, i.e., removed as input parameters of the query scripts.
• Refined user interface.
• Queue in web interface now reports region and isotimestamp for each queued query.
• Queries can be reached by knowing their ID only.
• Using newer version of JavaScript libraries.

Removed

• fprode_dbextract
• Single probe batch query interface.
• Query table from interface.