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46
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1 #!/usr/bin/env python
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2 import argparse
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54
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3 import os
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65
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4 import shutil
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46
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5
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6 import utils
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7
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54
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8 OUTPUT_DIR = 'assemblyPostProcessing_dir'
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9
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46
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10 parser = argparse.ArgumentParser()
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11 parser.add_argument('--dereplicate', dest='dereplicate', default=None, help='Remove duplicate sequences')
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12 parser.add_argument('--gap_trimming', dest='gap_trimming', type=float, default=0, help='Trim alignments')
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13 parser.add_argument('--gene_family_search', dest='gene_family_search', default=None, help='Targeted gene families')
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14 parser.add_argument('--method', dest='method', default=None, help='Protein clustering method')
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15 parser.add_argument('--min_length', dest='min_length', type=int, default=0, help='Minimum sequence length')
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16 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of processors')
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65
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17 parser.add_argument('--output_cds', dest='output_cds', help='Output transcripts.cds')
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18 parser.add_argument('--output_cleaned_cds', dest='output_cleaned_cds', help='Output transcripts.cleaned.cds')
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19 parser.add_argument('--output_cleaned_nr_cds', dest='output_cleaned_nr_cds', default=None, help='Output transcripts.cleaned.nr.cds')
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20 parser.add_argument('--output_cleaned_nr_pep', dest='output_cleaned_nr_pep', default=None, help='Output transcripts.cleaned.nr.pep')
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21 parser.add_argument('--output_cleaned_pep', dest='output_cleaned_pep', help='Output transcripts.cleaned.pep')
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22 parser.add_argument('--output_pep', dest='output_pep', help='Output transcripts.pep')
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83
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23 parser.add_argument('--output_targeted_gene_families_stats', dest='output_targeted_gene_families_stats', default=None, help='Targeted gene families statistics')
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46
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24 parser.add_argument('--prediction_method', dest='prediction_method', help='Coding regions prediction method')
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25 parser.add_argument('--scaffold', dest='scaffold', default=None, help='Gene family scaffold')
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26 parser.add_argument('--score_matrices', dest='score_matrices', default=None, help='Scores matrices')
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27 parser.add_argument('--strand_specific', dest='strand_specific', default=None, help='Strand-specific assembly')
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28 parser.add_argument('--transcripts', dest='transcripts', help='Transcriptome assembly fasta file')
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29
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30 args = parser.parse_args()
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31
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32 # Build the command line.
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33 cmd = 'AssemblyPostProcessor'
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34 if args.dereplicate is not None:
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35 cmd += ' --dereplicate'
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36 if args.gap_trimming > 0:
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37 cmd += ' --gap_trimming %4f' % args.gap_trimming
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38 if args.gene_family_search is not None:
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39 cmd += ' --gene_family_search %s' % args.gene_family_search
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40 if args.method is not None:
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41 cmd += ' --method %s' % args.method
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42 if args.min_length > 0:
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43 cmd += ' --min_length %d' % args.min_length
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44 cmd += ' --num_threads %d' % args.num_threads
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45 cmd += ' --prediction_method %s' % args.prediction_method
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46 if args.scaffold is not None:
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47 cmd += ' --scaffold %s' % args.scaffold
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48 if args.score_matrices is not None:
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49 cmd += ' --score_matrices %s' % args.score_matrices
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50 if args.strand_specific is not None:
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51 cmd += ' --strand_specific'
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52 cmd += ' --transcripts %s' % args.transcripts
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53 # Run the command.
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49
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54 utils.run_command(cmd)
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54
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55
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56 # Handle outputs.
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57 shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cds'), args.output_cds)
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58 shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cleaned.cds'), args.output_cleaned_cds)
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59 if args.output_cleaned_nr_cds is not None:
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60 shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cleaned.nr.cds'), args.output_cleaned_nr_cds)
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61 if args.output_cleaned_nr_pep is not None:
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62 shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cleaned.nr.pep'), args.output_cleaned_nr_pep)
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63 shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cleaned.pep'), args.output_cleaned_pep)
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64 shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.pep'), args.output_pep)
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83
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65 if args.output_targeted_gene_families_stats is not None:
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66 shutil.move(os.path.join(OUTPUT_DIR, 'targeted_gene_family_assemblies.stats'), args.output_targeted_gene_families_stats)
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