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1 #!/usr/bin/env python
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2 import argparse
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7
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3 import os
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4 import subprocess
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5
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6 import utils
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7
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8 OUTPUT_DIR = 'integratedGeneFamilies_dir'
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9
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10 parser = argparse.ArgumentParser()
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11 parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help="Directory of input fasta datasets")
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6
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12 parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold')
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13 parser.add_argument('--method', dest='method', help='Protein clustering method')
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14 parser.add_argument('--orthogroup_fna', dest='orthogroup_fna', default=None, help='Use correspong coding sequences')
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15 parser.add_argument('--output', dest='output', help="Output dataset")
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16 parser.add_argument('--output_dir', dest='output_dir', help="Output dataset file_path directory")
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17
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18 args = parser.parse_args()
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19
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20 # Build the command line.
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21 cmd = 'GeneFamilyIntegrator'
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22 cmd += ' --orthogroup_faa %s' % args.orthogroup_faa
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23 cmd += ' --scaffold %s' % args.scaffold
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24 cmd += ' --method %s' % args.method
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25 if args.orthogroup_fna is not None:
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26 cmd += ' --orthogroup_fna'
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27 # Run the command.
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28 proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)
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29 rc = proc.wait()
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30 utils.check_execution_errors(rc, proc.stderr)
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31 utils.move_directory_files(os.path.join(OUTPUT_DIR, 'orthogroups_fasta'), args.output_dir)
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32 utils.write_html_output(args.output, 'Integrated gene family sequences', args.output_dir)
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