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1 #!/usr/bin/env python
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2 import argparse
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3 import subprocess
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4
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5 import utils
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6
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7 OUTPUT_DIR = 'phylogenomicsAnalysis_dir'
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8
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9 parser = argparse.ArgumentParser()
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10
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11 parser.add_argument('--alignments_type', dest='alignments_type', help='Input alignments type produced by the GeneFamilyAligner')
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12 parser.add_argument('--bootstrap_replicates', dest='bootstrap_replicates', type=int, default=None, help='Number of replicates for rapid bootstrap analysis')
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13 parser.add_argument('--config_dir', dest='config_dir', help='Directory containing default configuration files')
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14 parser.add_argument('--max_orthogroup_size', dest='max_orthogroup_size', type=int, help='Maximum number of sequences in orthogroup alignments')
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15 parser.add_argument('--method', dest='method', help='Protein clustering method')
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16 parser.add_argument('--min_orthogroup_size', dest='min_orthogroup_size', type=int, help='Minimum number of sequences in orthogroup alignments')
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17 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
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18 parser.add_argument('--orthogroup_aln', dest='orthogroup_aln', help="Input dataset files_path")
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19 parser.add_argument('--output', dest='output', help='Output for phylogenetic trees')
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20 parser.add_argument('--output_dir', dest='output_dir', help='output.files_path')
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21 parser.add_argument('--rooting_order', dest='rooting_order', default=None, help='Rooting order configuration for rooting trees')
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22 parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold')
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23 parser.add_argument('--sequence_type', dest='sequence_type', help="Sequence type used in the phylogenetic inference")
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24 parser.add_argument('--tree_inference', dest='tree_inference', help='Phylogenetic trees inference method')
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25
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26 args = parser.parse_args()
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27
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28 # Build the command line.
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29 cmd = 'GeneFamilyPhylogenyBuilder'
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30 cmd += ' --alignment_type %s' % args.tree_inference
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31 if args.bootstrap_replicates is not None:
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32 cmd += ' --bootstrap_replicates %d' % args.bootstrap_replicates
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33 cmd += ' --config_dir %s' % args.config_dir
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34 cmd += ' --max_orthogroup_size %d' % args.max_orthogroup_size
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35 cmd += ' --method %s' % args.method
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36 cmd += ' --min_orthogroup_size %d' % args.min_orthogroup_size
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37 cmd += ' --num_threads %d' % args.num_threads
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38 cmd += ' --orthogroup_aln %s' % args.orthogroup_aln
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39 if args.rooting_order is not None:
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40 cmd += ' --rooting_order %s' % args.rooting_order
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41 cmd += ' --scaffold %s' % args.scaffold
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42 cmd += ' --sequence_type %s' % args.sequence_type
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43 cmd += ' --tree_inference %s' % args.tree_inference
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44 # Run the command.
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45 proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)
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46 rc = proc.wait()
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47 utils.check_execution_errors(rc, proc.stderr)
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48 utils.move_directory_files(OUTPUT_DIR, args.output_dir)
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49 utils.write_html_output(args.output, 'Phylogenetic trees', args.output_dir)
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