pyani.aniblastall module

Code to implement the ANIblastall average nucleotide identity method.

exception pyani.aniblastall.PyaniblastallException[source]

Bases: pyani.PyaniException

ANIblastall-specific exception for pyani.

pyani.aniblastall.get_version(blast_exe: pathlib.Path = PosixPath('blastall')) → str[source]

Return BLAST blastall version as a string.

Parameters:blast_exe – path to blastall executable

We expect blastall to return a string as, for example

$ blastall -version
[blastall 2.2.26] ERROR: Number of database sequences to show \
one-line descriptions for (V) [ersion] is bad or out of range [? to ?]

This is concatenated with the OS name.

The following circumstances are explicitly reported as strings

  • no executable at passed path
  • non-executable file at passed path (this includes cases where the user doesn’t have execute permissions on the file)
  • no version info returned
  • executable cannot be run on this OS