Python modules

Much of the functionality of ModPipe is implemented ‘behind the scenes’ by a set of Python modules. For reference, some of these modules are documented here.

• Handling of biological data
  • modpipe.sequence – Handling of amino acid sequences
• Data structures
  • modpipe.serialize – Serialization of data structures
• Errors
  • Error
  • FileFormatError
  • MissingBinaryError
• Fold assignment methods
  • modpipe.fold_assignment – Fold assignment methods
• Configuration
  • modpipe.config – Configuration file handling
  • modpipe.filesystem – ModPipe filesystem
  • modpipe.binaries – Locations of external binaries
  • modpipe.version – Version and copyright information
• Utilities
  • modpipe.crc64 – Simple cyclic redundancy check
  • modpipe.matrix2d – Simple 2D matrix class
• Wrappers for external binaries
  • modpipe.cdhit – Wrapper for CD-HIT
  • modpipe.ce – Wrapper for CE
  • modpipe.tmalign – Wrapper for TMAlign
• Testing
  • modpipe.test – Test framework