[med-svn] [Git][med-team/gubbins][upstream] New upstream version 3.3.3
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Feb 4 17:23:18 GMT 2024
Étienne Mollier pushed to branch upstream at Debian Med / gubbins
Commits:
1ef3ddb3 by Étienne Mollier at 2024-02-04T17:35:44+01:00
New upstream version 3.3.3
- - - - -
9 changed files:
- README.md
- + docs/gpt_gubbins_logo.png
- docs/gubbins_plotting.md
- python/gubbins/common.py
- python/gubbins/run_gubbins.py
- python/gubbins/tests/test_dependencies.py
- python/gubbins/tests/test_utils.py
- python/gubbins/treebuilders.py
- python/gubbins/utils.py
Changes:
=====================================
README.md
=====================================
@@ -1,11 +1,13 @@
-# Gubbins
+# Gubbins <img src='docs/gpt_gubbins_logo.png' align="right" height="250" />
**G**enealogies **U**nbiased **B**y recom**B**inations **I**n **N**ucleotide **S**equences
+<!-- badges: start -->
[](https://github.com/nickjcroucher/gubbins/blob/master/LICENSE)
[](https://academic.oup.com/nar/article/43/3/e15/2410982)
[](http://bioconda.github.io/recipes/gubbins/README.html)
[](https://codecov.io/gh/nickjcroucher/gubbins)
+<!-- badges: end -->
## Contents
* [Introduction](#introduction)
@@ -74,7 +76,7 @@ autoreconf -i
make
[sudo] make install
cd python
-[sudo] python3 -m pip install .
+[sudo] python3 -m pip install [--prefix=$PREFIX] .
```
Use `sudo` to install Gubbins system-wide. If you don't have the permissions, run `configure` with a prefix to install Gubbins in your home directory.
@@ -132,6 +134,17 @@ Gubbins is free software, licensed under [GPLv2](https://github.com/nickjcrouche
## Feedback/Issues
There is no specific support for development or maintenance of Gubbins. However, we will try to help you out if you report any issues about usage of the software to the [issues page](https://github.com/nickjcroucher/gubbins/issues).
+## Development plan
+Version 3 incorporates a number of features that were explicitly requested by users (e.g. plotting functions), improved the algorithm's accuracy (e.g. using joint ancestral reconstruction) and were commonly used in published analyses (e.g. using IQTREE2 for phylogeny construction).
+
+Future development will prioritise:
+- More efficient phylogenetic processing with modern python libraries
+- Parallelisation of recombination searches
+- Faster sequence reconstruction through hardware acceleration
+- Extension of existing analyses using phylogenetic placement
+
+If you believe there are other improvements that could be added, please describe them on the [issues page](https://github.com/nickjcroucher/gubbins/issues) and tag the suggestion as an "enhancement".
+
## Citation
If you use this software please cite:
[Croucher N. J., Page A. J., Connor T. R., Delaney A. J., Keane J. A., Bentley S. D., Parkhill J., Harris S.R.
=====================================
docs/gpt_gubbins_logo.png
=====================================
Binary files /dev/null and b/docs/gpt_gubbins_logo.png differ
=====================================
docs/gubbins_plotting.md
=====================================
@@ -97,7 +97,7 @@ These options provide flexibility with regard to the labelling of different comp
### Example
-Using files from the associated [FigShare repository](https://figshare.com/account/projects/130637/articles/24117117), we can replicate the analysis shown in [Kwun, Ion, Cheng *et al*](https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-022-01147-2) with the command:
+Using files from the associated [FigShare repository](https://dx.doi.org/10.6084/m9.figshare.24117117), we can replicate the analysis shown in [Kwun, Ion, Cheng *et al*](https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-022-01147-2) with the command:
```
plot_gubbins.R --tree serotype_3.tre --rec serotype_3_recombination.gff --annotation serotype_3_annotation.gff --meta serotype_3_metadata.csv --max-branch-length 500 --clades serotype_3_clades.csv --markup serotype_3_markup.csv --legend-height 0.35 --tree-axis-expansion 30 --markup-height 0.1 --heatmap-x-nudge 0.05 --heatmap-y-nudge -0.05 --output serotype_3.png
=====================================
python/gubbins/common.py
=====================================
@@ -744,13 +744,13 @@ def return_algorithm_choices(args,i):
def return_algorithm(algorithm_choice, model, input_args, node_labels = None, extra = None):
initialised_algorithm = None
if algorithm_choice == "fasttree":
- initialised_algorithm = FastTree(threads = input_args.threads, model = model, bootstrap = input_args.bootstrap, verbose = input_args.verbose, additional_args = extra)
+ initialised_algorithm = FastTree(threads = input_args.threads, model = model, seed = input_args.seed, bootstrap = input_args.bootstrap, verbose = input_args.verbose, additional_args = extra)
elif algorithm_choice == "raxml":
- initialised_algorithm = RAxML(threads = input_args.threads, model = model, bootstrap = input_args.bootstrap, internal_node_prefix = node_labels, verbose = input_args.verbose, additional_args = extra)
+ initialised_algorithm = RAxML(threads = input_args.threads, model = model, seed = input_args.seed, bootstrap = input_args.bootstrap, internal_node_prefix = node_labels, verbose = input_args.verbose, additional_args = extra)
elif algorithm_choice == "raxmlng":
- initialised_algorithm = RAxMLNG(threads = input_args.threads, model = model, bootstrap = input_args.bootstrap, internal_node_prefix = node_labels, verbose = input_args.verbose, additional_args = extra)
+ initialised_algorithm = RAxMLNG(threads = input_args.threads, model = model, seed = input_args.seed, bootstrap = input_args.bootstrap, internal_node_prefix = node_labels, verbose = input_args.verbose, additional_args = extra)
elif algorithm_choice == "iqtree":
- initialised_algorithm = IQTree(threads = input_args.threads, model = model, bootstrap = input_args.bootstrap, internal_node_prefix = node_labels, verbose = input_args.verbose, use_best = (model is None and input_args.best_model), additional_args = extra)
+ initialised_algorithm = IQTree(threads = input_args.threads, model = model, seed = input_args.seed, bootstrap = input_args.bootstrap, internal_node_prefix = node_labels, verbose = input_args.verbose, use_best = (model is None and input_args.best_model), additional_args = extra)
elif algorithm_choice == "rapidnj":
initialised_algorithm = RapidNJ(threads = input_args.threads, model = model, bootstrap = input_args.bootstrap, verbose = input_args.verbose, additional_args = extra)
elif algorithm_choice == "star":
=====================================
python/gubbins/run_gubbins.py
=====================================
@@ -76,6 +76,8 @@ def parse_input_args():
default = False, action = 'store_true')
treeGroup.add_argument('--sh-test', help='Perform an SH test of node likelihoods', default = False,
action = 'store_true')
+ treeGroup.add_argument('--seed', help='Set seed for reproducibility of analysis',
+ default = None, type = int)
modelGroup = parser.add_argument_group('Nucleotide substitution model options')
modelGroup.add_argument('--model', '-M', help='Nucleotide substitution model (not all available for all '
=====================================
python/gubbins/tests/test_dependencies.py
=====================================
@@ -79,6 +79,18 @@ class TestExternalDependencies(unittest.TestCase):
self.cleanup('multiple_recombinations')
assert exit_code == 0
+ def test_fasttree_seed(self):
+ exit_code = 1
+ parser = run_gubbins.parse_input_args()
+ common.parse_and_run(parser.parse_args(["--tree-builder", "fasttree",
+ "--verbose", "--iterations", "3",
+ "--seed","42",
+ "--threads", "1",
+ os.path.join(data_dir, 'multiple_recombinations.aln')]))
+ exit_code = self.check_for_output_files('multiple_recombinations')
+ self.cleanup('multiple_recombinations')
+ assert exit_code == 0
+
# Test resuming a default analysis
def test_fasttree_resume(self):
exit_code = 1
@@ -122,6 +134,18 @@ class TestExternalDependencies(unittest.TestCase):
self.cleanup('multiple_recombinations')
assert exit_code == 0
+ def test_iqtree_seed(self):
+ exit_code = 1
+ parser = run_gubbins.parse_input_args()
+ common.parse_and_run(parser.parse_args(["--tree-builder", "iqtree",
+ "--verbose", "--iterations", "3",
+ "--seed","42",
+ "--threads", "1",
+ os.path.join(data_dir, 'multiple_recombinations.aln')]))
+ exit_code = self.check_for_output_files('multiple_recombinations')
+ self.cleanup('multiple_recombinations')
+ assert exit_code == 0
+
def test_iqtree_custom_model(self):
exit_code = 1
parser = run_gubbins.parse_input_args()
@@ -246,6 +270,18 @@ class TestExternalDependencies(unittest.TestCase):
self.cleanup('multiple_recombinations')
assert exit_code == 0
+ def test_raxml_seed(self):
+ exit_code = 1
+ parser = run_gubbins.parse_input_args()
+ common.parse_and_run(parser.parse_args(["--tree-builder", "raxml",
+ "--verbose", "--iterations", "3",
+ "--seed","42",
+ "--threads", "1",
+ os.path.join(data_dir, 'multiple_recombinations.aln')]))
+ exit_code = self.check_for_output_files('multiple_recombinations')
+ self.cleanup('multiple_recombinations')
+ assert exit_code == 0
+
def test_raxml_custom_model(self):
exit_code = 1
parser = run_gubbins.parse_input_args()
@@ -301,6 +337,19 @@ class TestExternalDependencies(unittest.TestCase):
self.cleanup('multiple_recombinations')
assert exit_code == 0
+ def test_raxmlng_seed(self):
+ exit_code = 1
+ parser = run_gubbins.parse_input_args()
+ common.parse_and_run(parser.parse_args(["--tree-builder", "raxmlng",
+ "--model","GTR",
+ "--verbose", "--iterations", "3",
+ "--seed","42",
+ "--threads", "1",
+ os.path.join(data_dir, 'multiple_recombinations.aln')]))
+ exit_code = self.check_for_output_files('multiple_recombinations')
+ self.cleanup('multiple_recombinations')
+ assert exit_code == 0
+
def test_raxmlng_custom_model(self):
exit_code = 1
parser = run_gubbins.parse_input_args()
=====================================
python/gubbins/tests/test_utils.py
=====================================
@@ -107,3 +107,9 @@ class TestUtilities(unittest.TestCase):
printer.print(["AAA", "BBB"])
printed = f.getvalue()
assert printed == "AAA-BBB\n"
+
+ def test_seed(self):
+ set_seed_val = utils.set_seed(42)
+ assert set_seed_val == "42"
+ random_seed_val = utils.set_seed(None)
+ assert(int(random_seed_val) < 10001)
=====================================
python/gubbins/treebuilders.py
=====================================
@@ -20,7 +20,6 @@
import sys
import os
import subprocess
-from random import randint
from Bio import SeqIO
@@ -129,7 +128,7 @@ class RapidNJ:
class FastTree:
"""Class for operations with the FastTree executable"""
- def __init__(self, threads: int, bootstrap = 0, model='GTRCAT', verbose=False, additional_args = None):
+ def __init__(self, threads: int, bootstrap = 0, model='GTRCAT', seed = None, verbose=False, additional_args = None):
"""Initialises the object"""
self.verbose = verbose
self.threads = threads
@@ -139,9 +138,10 @@ class FastTree:
self.alignment_suffix = ".snp_sites.aln"
self.bootstrap = bootstrap
self.additional_args = additional_args
+ self.seed = utils.set_seed(seed)
# Identify executable
- self.potential_executables = ["FastTree", "fasttree"]
+ self.potential_executables = ["FastTreeMP","fasttreeMP","FastTree", "fasttree"]
self.executable = utils.choose_executable(self.potential_executables)
if self.executable is None:
sys.exit("No usable version of FastTree could be found.")
@@ -164,6 +164,7 @@ class FastTree:
command.extend(["-gtr"])
else:
command.extend([self.model])
+ command.extend(["-seed",self.seed])
# Additional arguments
if self.additional_args is not None:
command.extend([self.additional_args])
@@ -256,7 +257,7 @@ class FastTree:
class IQTree:
"""Class for operations with the IQTree executable"""
- def __init__(self, threads: 1, model: str, bootstrap = 0, internal_node_prefix="", verbose=False, use_best=False, additional_args = None):
+ def __init__(self, threads: 1, model: str, bootstrap = 0, seed = None, internal_node_prefix="", verbose=False, use_best=False, additional_args = None):
"""Initialises the object"""
self.verbose = verbose
self.threads = threads
@@ -271,6 +272,7 @@ class IQTree:
self.internal_node_prefix = internal_node_prefix
self.bootstrap = bootstrap
self.use_best = use_best
+ self.seed = utils.set_seed(seed)
self.additional_args = additional_args
# Construct base command
@@ -303,6 +305,7 @@ class IQTree:
command.extend(["-m","GTR+G4"])
else:
command.extend(["-m",self.model])
+ command.extend(["-seed",self.seed])
# Additional arguments
if self.additional_args is not None:
command.extend([self.additional_args])
@@ -432,7 +435,7 @@ class IQTree:
class RAxML:
"""Class for operations with the RAxML executable"""
- def __init__(self, threads: 1, model='GTRCAT', bootstrap = 0, internal_node_prefix="", verbose=False, additional_args = None):
+ def __init__(self, threads: 1, model='GTRCAT', bootstrap = 0, seed = None, internal_node_prefix="", verbose=False, additional_args = None):
"""Initialises the object"""
self.verbose = verbose
self.threads = threads
@@ -446,6 +449,7 @@ class RAxML:
self.alignment_suffix = ".phylip"
self.internal_node_prefix = internal_node_prefix
self.bootstrap = bootstrap
+ self.seed = utils.set_seed(seed)
self.additional_args = additional_args
self.single_threaded_executables = ['raxmlHPC-AVX2', 'raxmlHPC-AVX', 'raxmlHPC-SSE3', 'raxmlHPC']
@@ -465,9 +469,6 @@ class RAxML:
if self.threads > 1:
command.extend(["-T", str(self.threads)])
- # Set a seed
- command.extend(["-p",str(randint(0, 10000))])
-
# Add flags
command.extend(["-safe"])
if self.model == 'JC':
@@ -482,6 +483,7 @@ class RAxML:
command.extend(["-m","GTRGAMMA"])
else:
command.extend(["-m", self.model])
+ command.extend(["-p",self.seed])
# Additional arguments
if self.additional_args is not None:
command.extend([self.additional_args])
@@ -579,9 +581,7 @@ class RAxML:
command = self.base_command.copy()
command.extend(["-s", alignment_filename, "-n", basename + ".bootstrapped_trees"])
command.extend(["-w",tmp])
- p_seed = str(randint(0, 10000))
- command.extend(["-p",p_seed])
- command.extend(["-x",p_seed])
+ command.extend(["-x",self.seed])
command.extend(["-#",str(self.bootstrap)])
# Output
if not self.verbose:
@@ -592,8 +592,6 @@ class RAxML:
def sh_test(self, alignment_filename: str, input_tree: str, basename: str, tmp: str) -> str:
"""Runs a single branch support test"""
command = self.base_command.copy()
- p_seed = str(randint(0, 10000))
- command.extend(["-p",p_seed])
command.extend(["-f", "J"])
command.extend(["-s", alignment_filename, "-n", input_tree + ".sh_support"])
command.extend(["-t", input_tree])
@@ -610,7 +608,7 @@ class RAxML:
class RAxMLNG:
"""Class for operations with the RAxML executable"""
- def __init__(self, threads: 1, model: str, bootstrap = 0, internal_node_prefix = "", verbose = False, additional_args = None):
+ def __init__(self, threads: 1, model: str, bootstrap = 0, seed = None, internal_node_prefix = "", verbose = False, additional_args = None):
"""Initialises the object"""
self.verbose = verbose
self.threads = threads
@@ -624,6 +622,7 @@ class RAxMLNG:
self.alignment_suffix = ".phylip"
self.internal_node_prefix = internal_node_prefix
self.bootstrap = bootstrap
+ self.seed = utils.set_seed(seed)
self.additional_args = additional_args
self.single_threaded_executables = ['raxml-ng']
@@ -655,6 +654,7 @@ class RAxMLNG:
command.extend(["GTR+G"])
else:
command.extend([self.model])
+ command.extend(["--seed",self.seed])
# Additional arguments
if self.additional_args is not None:
command.extend([self.additional_args])
=====================================
python/gubbins/utils.py
=====================================
@@ -23,6 +23,7 @@ import subprocess
import re
import numpy as np
import collections
+from random import randint
try:
from multiprocessing.managers import SharedMemoryManager
NumpyShared = collections.namedtuple('NumpyShared', ('name', 'shape', 'dtype'))
@@ -195,3 +196,11 @@ def extend_args(var,add):
var.extend([add])
var = " ".join(var)
return var
+
+def set_seed(seed):
+ """Set seed when specified"""
+ if seed is None:
+ seed = str(randint(0, 10000))
+ else:
+ seed = str(seed)
+ return seed
View it on GitLab: https://salsa.debian.org/med-team/gubbins/-/commit/1ef3ddb3c4df977af600223e5113b0f4ed3b980d
--
View it on GitLab: https://salsa.debian.org/med-team/gubbins/-/commit/1ef3ddb3c4df977af600223e5113b0f4ed3b980d
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