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1 #!/usr/bin/env python
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2 import argparse
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19
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3 import os
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4
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5 import utils
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6
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19
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7 OUTPUT_DIR = 'geneFamilyPhylogenies_dir'
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8
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9 parser = argparse.ArgumentParser()
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10
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5
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11 parser.add_argument('--alignment_type', dest='alignment_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_phylip', dest='output_phylip', default=None, help='Output for orthogroup phylip multiple sequence alignments')
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20 parser.add_argument('--output_phylip_dir', dest='output_phylip_dir', default=None, help='output_phylip.files_path')
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21
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21 #parser.add_argument('--output_tree', dest='output_tree', help='Output for phylogenetic trees')
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22 #parser.add_argument('--output_tree_dir', dest='output_tree_dir', help='output_tree.files_path')
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23 parser.add_argument('--rooting_order', dest='rooting_order', default=None, help='Rooting order configuration for rooting trees')
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24 parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold')
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25 parser.add_argument('--sequence_type', dest='sequence_type', help='Sequence type used in the phylogenetic inference')
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26 parser.add_argument('--tree_inference', dest='tree_inference', help='Phylogenetic trees inference method')
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27
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28 args = parser.parse_args()
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29
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30 # Build the command line.
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31 cmd = 'GeneFamilyPhylogenyBuilder'
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32 cmd += ' --alignment_type %s' % args.alignment_type
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33 if args.bootstrap_replicates is not None:
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34 cmd += ' --bootstrap_replicates %d' % args.bootstrap_replicates
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35 cmd += ' --config_dir %s' % args.config_dir
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36 cmd += ' --max_orthogroup_size %d' % args.max_orthogroup_size
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37 cmd += ' --method %s' % args.method
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38 cmd += ' --min_orthogroup_size %d' % args.min_orthogroup_size
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39 cmd += ' --num_threads %d' % args.num_threads
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40 cmd += ' --orthogroup_aln %s' % args.orthogroup_aln
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41 if args.rooting_order is not None:
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42 cmd += ' --rooting_order %s' % args.rooting_order
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43 cmd += ' --scaffold %s' % args.scaffold
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44 cmd += ' --sequence_type %s' % args.sequence_type
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45 cmd += ' --tree_inference %s' % args.tree_inference
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46
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47 # Run the command.
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48 utils.run_command(cmd)
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49
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50 # Handle outputs.
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51 if args.output_phylip is not None and args.output_phylip_dir is not None:
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52 src_output_dir = os.path.join(OUTPUT_DIR, 'phylip_aln')
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53 utils.move_directory_files(src_output_dir, args.output_phylip_dir)
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54 utils.write_html_output(args.output_phylip, 'Orthogroup phylip multiple sequence alignments', args.output_phylip_dir)
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55 #src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_tree')
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56 #utils.move_directory_files(src_output_dir, args.output_tree_dir)
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57 #utils.write_html_output(args.output_tree, 'Phylogenetic trees', args.output_tree_dir)
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