Coverage for PanACoTA/tree_module/fastme

1#!/usr/bin/env python3

2# coding: utf-8

4# ###############################################################################

5# This file is part of PanACOTA. #

6# #

7# Authors: Amandine Perrin #

9# See the COPYRIGHT file for details. #

10# #

11# PanACOTA is a software providing tools for large scale bacterial comparative #

12# genomics. From a set of complete and/or draft genomes, you can: #

13# - Do a quality control of your strains, to eliminate poor quality #

14# genomes, which would not give any information for the comparative study #

15# - Uniformly annotate all genomes #

16# - Do a Pan-genome #

17# - Do a Core or Persistent genome #

18# - Align all Core/Persistent families #

19# - Infer a phylogenetic tree from the Core/Persistent families #

20# #

21# PanACOTA is free software: you can redistribute it and/or modify it under the #

22# terms of the Affero GNU General Public License as published by the Free #

23# Software Foundation, either version 3 of the License, or (at your option) #

24# any later version. #

25# #

26# PanACOTA is distributed in the hope that it will be useful, but WITHOUT ANY #

27# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS #

28# FOR A PARTICULAR PURPOSE. See the Affero GNU General Public License #

29# for more details. #

30# #

31# You should have received a copy of the Affero GNU General Public License #

32# along with PanACOTA (COPYING file). #

33# If not, see <https://www.gnu.org/licenses/>. #

34# ###############################################################################

36"""

37Functions to infer a phylogenetic tree with fastME

39@author gem

40June 2017

41"""

43from Bio import AlignIO

44import os

45import logging

47from PanACoTA import utils

49logger = logging.getLogger("tree.fastme")

51def run_tree(alignfile, boot, outdir, quiet, threads, **kwargs):

52 """

53 Run fastme for the given alignment file and options

55 Parameters

56 ----------

57 alignfile: str

58 Path to file containing alignments of persistent families grouped by genome

59 boot: int or None

60 Number of bootstraps to compute. None if no bootstrap asked

61 outdir: str

62 output directory to save all results

63 quiet: bool

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

65 threads: int

66 Maximum number of threads to use

67 kwargs["model"]: str

68 DNA substitution model chosen by user

69 kwargs["matrix"]: bool

70 True if matrix file must be written, False otherwise

71 kwargs["wb"]: bool

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

73 """

74 model = kwargs["model"]

75 write_boot = kwargs["wb"]

76 write_matrix = kwargs["matrix"]

77 align_name = os.path.basename(alignfile)

78 align_phylip = os.path.join(outdir, align_name + ".phylip")

79 convert2phylip(alignfile, align_phylip)

80 run_fastme(align_phylip, boot, write_boot, write_matrix, threads, model, outdir, quiet)

83def convert2phylip(infile, outfile):

84 """

85 Input alignment is in fasta format. Input of fastME must be in Phylip-relaxed format.

86 Convert it here.

88 Parameters

89 ----------

90 infile: str

91 Path to file in fasta format

92 outfile: str

93 Path to file to generate, in Phylip-relaxed format

94 """

95 if os.path.isfile(outfile):

96 logger.info("Phylip alignment file already existing.")

97 logger.warning(("The Phylip alignment file {} already exists. The program "

98 "will use it instead of re-converting {}.").format(outfile, infile))

99 return

100 logger.info("Converting fasta alignment to PHYLIP-relaxed format.")

101 with open(infile, 'r') as input_handle, open(outfile, 'w') as output_handle:

102 alignments = AlignIO.parse(input_handle, "fasta")

103 AlignIO.write(alignments, output_handle, "phylip-relaxed")

104

105

106def run_fastme(alignfile, boot, write_boot, write_matrix, threads, model, outdir, quiet):

107 """

108 Run fastME on the given alignment.

109

110 Parameters

111 ----------

112 alignfile: str

113 Path to file containing alignments of persistent families grouped by genome

114 boot: int or None

115 Number of bootstraps to compute. None if no bootstrap asked

116 write_boot: bool

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

118 threads: int

119 Maximum number of threads to use

120 model: str or None

121 DNA substitution model chosen by user. None if default one

122 outdir: str

123 output directory to save all results

124 quiet: bool

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

126 """

127 logger.info("Running FastME...")

128 bootinfo = ""

129 threadinfo = ""

130 outboot = ""

131 outmat = ""

132

133 # Get bootstrap information

134 if boot:

135 bootinfo = "-b {}".format(boot)

136 # Get threads information

137 if threads:

138 threadinfo = "-T {}".format(threads)

139 # Get output filename

140 align_name = os.path.basename(alignfile)

141 logfile = os.path.join(outdir, align_name + ".fastme.log")

142 treefile = os.path.join(outdir, align_name + ".fastme_tree.nwk")

143 # If bootstrap pseudo-trees must be written, define the filename here

144 if write_boot:

145 outboot = "-B " + os.path.join(outdir, align_name + ".fastme_bootstraps.nwk")

146 if write_matrix:

147 outmat = "-O " + os.path.join(outdir, align_name + ".fastme_dist-mat.txt")

148 # Put default model if not given

149 if not model:

150 model = "T"

151 cmd = (f"fastme -i {alignfile} -d {model} -n B -s {threadinfo} {bootinfo} "

152 f"-o {treefile} -I {logfile} {outboot} {outmat}")

153 logger.details(cmd)

154 if quiet:

155 fnull = open(os.devnull, 'w')

156 else:

157 fnull = None

158 error = ("Problem while running FastME. See log file ({}) for "

159 "more information.").format(logfile)

160 utils.run_cmd(cmd, error, stdout=fnull, eof=True, logger=logger, stderr=fnull)

Coverage for PanACoTA/tree_module/fastme_func.py: 100%

49 statements