Bio.Phylo.PAML.yn00 module

Classes for the support of YN00.

Yang and Nielsen 2000, estimating synonymous and nonsynonymous substitution rates in pairwise comparison of protein-coding DNA sequences.

exception Bio.Phylo.PAML.yn00.Yn00Error

Bases: OSError

YN00 failed. Run with verbose=True to view YN00’s error message.

class Bio.Phylo.PAML.yn00.Yn00(alignment=None, working_dir=None, out_file=None)

Bases: Paml

An interface to YN00, part of the PAML package.

__init__(alignment=None, working_dir=None, out_file=None)

Initialize the Yn00 instance.

The user may optionally pass in strings specifying the locations of the input alignment, the working directory and the final output file.

write_ctl_file()

Dynamically build a YN00 control file from the options.

The control file is written to the location specified by the ctl_file property of the Yn00 class.

read_ctl_file(ctl_file)

Parse a control file and load the options into the Yn00 instance.

Update each YN00 option to the new option if supplied or None if not supplied. Raise an exception if the control file does not exist, a line is malformed, or an option is invalid.

run(ctl_file=None, verbose=False, command='yn00', parse=True)

Run yn00 using the current configuration.

If parse is True then read and return the result, otherwise return None. An exception is raised if the return code of the yn00 command is non-zero.

__annotations__ = {}

Bio.Phylo.PAML.yn00.read(results_file)

Parse a YN00 results file.

Return the results if there are any. Raise an exception if the results file does not exist, is empty, or is invalid.