PanACoTA.tree_module package

PanACoTA tree_module

fastme_func submodule

Functions to infer a phylogenetic tree with fastME

@author gem June 2017

PanACoTA.tree_module.fastme_func.convert2phylip(infile, outfile)

Input alignment is in fasta format. Input of fastME must be in Phylip-relaxed format. Convert it here.

Parameters:
infile: str

Path to file in fasta format

outfile: str

Path to file to generate, in Phylip-relaxed format

PanACoTA.tree_module.fastme_func.run_fastme(alignfile, boot, write_boot, write_matrix, threads, model, outdir, quiet)

Run fastME on the given alignment.

Parameters:
alignfile: str

Path to file containing alignments of persistent families grouped by genome

boot: int or None

Number of bootstraps to compute. None if no bootstrap asked

write_boot: bool

True if all bootstrap pseudo-trees must be saved into a file, False otherwise

threads: int

Maximum number of threads to use

model: str or None

DNA substitution model chosen by user. None if default one

outdir: str

output directory to save all results

quiet: bool

True if nothing must be printed to stderr/stdout, False otherwise

PanACoTA.tree_module.fastme_func.run_tree(alignfile, boot, outdir, quiet, threads, **kwargs)

Run fastme for the given alignment file and options

Parameters:
alignfile: str

Path to file containing alignments of persistent families grouped by genome

boot: int or None

Number of bootstraps to compute. None if no bootstrap asked

outdir: str

output directory to save all results

quiet: bool

True if nothing must be printed to stderr/stdout, False otherwise

threads: int

Maximum number of threads to use

kwargs[“model”]: str

DNA substitution model chosen by user

kwargs[“matrix”]: bool

True if matrix file must be written, False otherwise

kwargs[“wb”]: bool

True if all bootstrap pseudo-trees must be saved into a file, False otherwise

fasttree_func submodule

Function to infer a phylogenetic tree from a persistent genome, using FastTree

@author gem June 2017

PanACoTA.tree_module.fasttree_func.define_nb_threads(threads)

With FastTree, number of threads to use must be defined before running the script, by changing an environment variable.

Parameters:
threads: int

Maximal number of threads to use

PanACoTA.tree_module.fasttree_func.run_fasttree(alignfile, boot, outdir, model, quiet)

Run FastTree on given alignment

Parameters:
alignfile: str

Path to file containing all families aligned, grouped by genome

boot: int or None

Number of bootstraps to calculate (None if no bootstrap asked)

treefile: str or None

Path to the tree file that must be created

model: str

DNA substitution model

quiet: bool

True if nothing must be printed to stderr/stdout, False otherwise

PanACoTA.tree_module.fasttree_func.run_tree(alignfile, boot, outdir, quiet, threads, **kwargs)

Run FastTree for the given alignment file and options

Parameters:
alignfile: str

path to file containing all persistent families aligned, and grouped by genome

boot: int or None

number of bootstraps to calculate, None if no bootstrap asked

outdir: str or None

Path to the tree file that must be created

quiet: bool

True if nothing must be printed to stderr/stdout, False otherwise

threads: int

Maximum number of threads to use

model: str

DNA substitution model chosen by user

kwargs: Object

Used to be compatible with the ‘run_tree’ function of other softs like fastME and quicktree, which require more arguments

quicktree_func submodule

Functions to infer a phylogenetic tree with quicktree

@author gem June 2017

PanACoTA.tree_module.quicktree_func.convert2stockholm(infile, outfile)

Input alignment is in fasta format. Input of quicktree must be in stockholm format. Convert it here.

Parameters:
infile: str

Path to file containing alignments in fasta

outfile: str

Path to file which will contain the alignments converted to Stockholm format

PanACoTA.tree_module.quicktree_func.run_quicktree(alignfile, boot, outdir)

Run quicktree on the given alignment.

Parameters:
alignfile: str

Path to file containing alignments of persistent families grouped by genome, in Stockholm format

boot: int or None

Number of bootstraps to compute. None if no bootstrap asked

outdir: str or None

Path to the tree file that must be created

PanACoTA.tree_module.quicktree_func.run_tree(alignfile, boot, outdir, *args, **kwargs)

Run quicktree for the given alignment file and options

Parameters:
alignfile: str

Path to file containing alignments of persistent families grouped by genome

boot: int or None

Number of bootstraps to compute. None if no bootstrap asked

outdir: str or None

Path to the tree file that must be created

args: tuple

Used to be compatible with the ‘run_tree’ function of other softs like fastME and fastTree which require more arguments like the DNA substitution model, the number of threads to use, etc.

kwargs: dict

Used to be compatible with the ‘run_tree’ function of other softs like fastME and fastTree which require more arguments like the DNA substitution model, the number of threads to use, etc.