.. _wrappers: -------------------------- External application tools -------------------------- This module contains functions that can run external programs within the EggLib framework (taking as arguments and/or returning EggLib objects). To use these functions, the underlying programs must be available in the system. This is controlled by the application paths object as explained in :ref:`apps`. .. autosummary:: egglib.wrappers.phyml egglib.wrappers.codeml egglib.wrappers.nj egglib.wrappers.clustal egglib.wrappers.muscle egglib.wrappers.makeblastdb egglib.wrappers.megablast egglib.wrappers.dc_megablast egglib.wrappers.blastn egglib.wrappers.blastn_short egglib.wrappers.blastp egglib.wrappers.blastp_short egglib.wrappers.blastp_fast egglib.wrappers.blastx egglib.wrappers.blastx_fast egglib.wrappers.tblastn egglib.wrappers.tblastn_fast egglib.wrappers.tblastx egglib.wrappers.BlastHit egglib.wrappers.BlastHsp egglib.wrappers.BlastOutput egglib.wrappers.BlastQueryHits .. autofunction:: egglib.wrappers.phyml .. autofunction:: egglib.wrappers.codeml .. autofunction:: egglib.wrappers.nj .. autofunction:: egglib.wrappers.clustal .. autofunction:: egglib.wrappers.muscle .. autofunction:: egglib.wrappers.muscle5 .. autofunction:: egglib.wrappers.muscle3 .. autofunction:: egglib.wrappers.makeblastdb .. autofunction:: egglib.wrappers.megablast .. autofunction:: egglib.wrappers.dc_megablast .. autofunction:: egglib.wrappers.blastn .. autofunction:: egglib.wrappers.blastn_short .. autofunction:: egglib.wrappers.blastp .. autofunction:: egglib.wrappers.blastp_short .. autofunction:: egglib.wrappers.blastp_fast .. autofunction:: egglib.wrappers.blastx .. autofunction:: egglib.wrappers.blastx_fast .. autofunction:: egglib.wrappers.tblastn .. autofunction:: egglib.wrappers.tblastn_fast .. autofunction:: egglib.wrappers.tblastx .. autoclass:: egglib.wrappers.BlastOutput :members: .. autoclass:: egglib.wrappers.BlastQueryHits :members: .. autoclass:: egglib.wrappers.BlastHit :members: .. autoclass:: egglib.wrappers.BlastHsp :members: .. _paths: Configuring paths ----------------- Application paths can be set using the following syntax. A :exc:`ValueError` is raised if the automatic test fails. The change is valid for the current session only unless :meth:`.save` is used:: egglib.wrappers.paths[app] = path And application paths are accessed as followed:: egglib.wrappers.paths[app] .. method:: egglib.wrappers.paths.autodetect(verbose=False) Auto-configure application paths based on default command names. :param verbose: if ``True``, print progress information. The function returns a ``(npassed, nfailed, failed_info)`` with: * ``npassed`` the number of applications which passed. * ``nfailed`` the number of applications which failed. * ``failed_info`` a :class:`dict` containing, for each failing application, the command which was used and the error message. .. method:: egglib.wrappers.path.load Load values of application paths from the configuration file located within the package. All values currently set are discarded. .. method:: egglib.wrappers.path.save Save current values of application paths in the configuration file located within the package. This action may require administrator rights. All values currently set will be reloaded at next import of the package. .. _blastn-options: