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Updated docstrings to include the output and mention any validation that occurs. Also, changed docstring so they have consistent capitalization. Baseml >> BASEML etc

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This commit is contained in:
funcylambda
2018-10-06 10:13:58 +01:00
committed by Peter Cock
parent 6851cd8d03
commit 95f8119ad9
2 changed files with 28 additions and 12 deletions
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18
Bio/Phylo/PAML/baseml.py
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@ -69,7 +69,7 @@ class Baseml(Paml):
"""Dynamically build a BASEML control file from the options.
The control file is written to the location specified by the
ctl_file property of the baseml class.
ctl_file property of the BASEML class.
"""
# Make sure all paths are relative to the working directory
self._set_rel_paths()
@ -100,7 +100,11 @@ class Baseml(Paml):
ctl_handle.write(f"{option[0]} = {option[1]}\n")
def read_ctl_file(self, ctl_file):
"""Parse a control file and load the options into the Baseml instance."""
"""Parse a control file and load the options into the BASEML instance.
Check that the file exists and that the lines in the file are valid.
Then update each BASEML options to the new option if supplied or None
if not supplied. Otherwise raise an exception."""
temp_options = {}
if not os.path.isfile(ctl_file):
raise FileNotFoundError(f"File not found: {ctl_file!r}")
@ -167,8 +171,8 @@ class Baseml(Paml):
"""Run baseml using the current configuration.
Check that the tree attribute is specified and exists, and then
run baseml. If parse is True then read and return the result,
otherwise return none.
run BASEML. If parse is True then read and return the result. If
parse is False return None. Otherwise raise an exception.
The arguments may be passed as either absolute or relative paths,
despite the fact that BASEML requires relative paths.
@ -184,7 +188,11 @@ class Baseml(Paml):
def read(results_file):
"""Parse a BASEML results file."""
"""Parse a BASEML results file.
Check that the file exits, that the results file is not empty, and then
parse the file. Check there is a version in the results and then return
the results. Otherwise raise an exception."""
results = {}
if not os.path.exists(results_file):
raise FileNotFoundError("Results file does not exist.")

22
Bio/Phylo/PAML/codeml.py
View File

@ -24,7 +24,7 @@ class Codeml(Paml):
"""An interface to CODEML, part of the PAML package."""
def __init__(self, alignment=None, tree=None, working_dir=None, out_file=None):
"""Initialize the codeml instance.
"""Initialize the Codeml instance.
The user may optionally pass in strings specifying the locations
of the input alignment and tree files, the working directory and
@ -74,7 +74,7 @@ class Codeml(Paml):
"""Dynamically build a CODEML control file from the options.
The control file is written to the location specified by the
ctl_file property of the codeml class.
ctl_file property of the CODEML class.
"""
# Make sure all paths are relative to the working directory
self._set_rel_paths()
@ -98,7 +98,11 @@ class Codeml(Paml):
ctl_handle.write(f"{option[0]} = {option[1]}\n")
def read_ctl_file(self, ctl_file):
"""Parse a control file and load the options into the Codeml instance."""
"""Parse a control file and load the options into the CODEML instance.
Check that the file exists and that the lines in the file are valid.
Then update each CODEML options to the new option if supplied or None
if not supplied. Otherwise raise an exception."""
temp_options = {}
if not os.path.isfile(ctl_file):
raise FileNotFoundError(f"File not found: {ctl_file!r}")
@ -175,10 +179,11 @@ class Codeml(Paml):
self._rel_tree = os.path.relpath(self.tree, self.working_dir)
def run(self, ctl_file=None, verbose=False, command="codeml", parse=True):
"""Run codeml using the current configuration.
"""Run CODEML using the current configuration.
If parse is True then read and return the results, otherwise
return None.
Check that the tree attribute is specified and exists, and then
run CODEML. If parse is True then read and return the results. If
parse is false return None. Otherwise raise an exception.
The arguments may be passed as either absolute or relative
paths, despite the fact that CODEML requires relative paths.
@ -194,7 +199,10 @@ class Codeml(Paml):
def read(results_file):
"""Parse a CODEML results file."""
"""Parse a CODEML results file.
Check that the file exists and is not empty. Return the results
if there are any. Otherwise raise an exception."""
results = {}
if not os.path.exists(results_file):
raise FileNotFoundError("Results file does not exist.")