Mercurial > repos > yating-l > jbrowse_hub
annotate jbrowse_hub.py @ 28:5580dbf2a31c draft
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit e81fecac281f299db00cfc88a068e056b031ae9d-dirty
author | yating-l |
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date | Wed, 15 Mar 2017 11:36:09 -0400 |
parents | a4a54b925c73 |
children | d8049deb0c97 |
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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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1 #!/usr/bin/env python |
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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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2 |
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3 import os |
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4 import sys |
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5 import argparse |
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6 import subprocess |
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7 from bedToGff3 import bedToGff3 |
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8 import blastxmlToGff3 |
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9 import utils |
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10 import tempfile |
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11 import trackObject |
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12 import TrackHub |
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13 import shutil |
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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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14 |
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15 def main(argv): |
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16 parser = argparse.ArgumentParser(description='Create a hub to display in jbrowse.') |
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17 |
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18 # Reference genome mandatory |
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19 parser.add_argument('-f', '--fasta', help='Fasta file of the reference genome') |
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20 |
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21 # Genome name |
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22 parser.add_argument('-g', '--genome_name', help='Name of reference genome') |
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23 |
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24 # Output folder |
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25 parser.add_argument('-o', '--out', help='output html') |
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26 |
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27 # Output folder |
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28 parser.add_argument('-e', '--extra_files_path', help="Directory of JBrowse Hub folder") |
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29 |
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30 # GFF3 structure: gene->transcription->CDS |
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31 parser.add_argument('--gff3_transcript', action='append', help='GFF3 format, structure: gene->transcription->CDS') |
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32 |
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33 # GFF3 structure: gene->mRNA->CDS |
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34 parser.add_argument('--gff3_mrna', action='append', help='GFF3 format, structure: gene->mRNA->CDS') |
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35 |
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36 # trfBig simple repeats (BED 4+12) |
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37 parser.add_argument('--bedSimpleRepeats', action='append', help='BED 4+12 format, using simpleRepeats.as') |
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38 |
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39 # regtools (BED 12+1) |
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40 parser.add_argument('--bedSpliceJunctions', action='append', help='BED 12+1 format, using spliceJunctions.as') |
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41 |
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42 # tblastn alignment (blastxml) |
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43 parser.add_argument('--blastxml', action='append', help='blastxml format from tblastn') |
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44 |
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45 # BAM format |
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46 parser.add_argument('--bam', action='append', help='BAM format from HISAT') |
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47 |
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48 # BIGWIG format |
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49 parser.add_argument('--bigwig', action='append', help='BIGWIG format to show rnaseq coverage') |
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50 |
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51 # GTF format |
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52 parser.add_argument('--gtf', action='append', help='GTF format from StringTie') |
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53 |
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54 args = parser.parse_args() |
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55 all_datatype_dictionary = dict() |
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56 |
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57 |
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58 reference = args.fasta |
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59 genome = 'unknown' |
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60 out_path = '.' |
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61 extra_files_path = '.' |
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62 if args.genome_name: |
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63 genome = utils.sanitize_name_path(args.genome_name) |
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64 if args.out: |
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65 out_path = args.out |
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66 if args.extra_files_path: |
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67 extra_files_path = utils.sanitize_name_path(args.extra_files_path) |
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68 cwd = os.getcwd() |
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69 #tool_directory not work for Galaxy tool, all tools need to exist in the current PATH, deal with it with tool dependencies |
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70 tool_directory = os.path.join(cwd, 'JBrowse-1.12.1/bin') |
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71 chrom_size = utils.getChromSizes(reference, tool_directory) |
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72 all_tracks = trackObject.trackObject(chrom_size.name, genome, extra_files_path) #store converted files in the array: all_tracks.tracks |
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73 array_inputs_bam = args.bam |
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74 array_inputs_bed_simple_repeats = args.bedSimpleRepeats |
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75 array_inputs_bed_splice_junctions = args.bedSpliceJunctions |
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76 array_inputs_bigwig = args.bigwig |
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77 array_inputs_gff3_transcript = args.gff3_transcript |
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78 array_inputs_gff3_mrna = args.gff3_mrna |
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79 array_inputs_gtf = args.gtf |
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80 array_inputs_blastxml = args.blastxml |
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81 if array_inputs_bam: |
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82 all_datatype_dictionary['bam'] = array_inputs_bam |
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83 if array_inputs_bed_simple_repeats: |
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84 all_datatype_dictionary['bedSimpleRepeats'] = array_inputs_bed_simple_repeats |
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85 if array_inputs_bed_splice_junctions: |
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86 all_datatype_dictionary['bedSpliceJunctions'] = array_inputs_bed_splice_junctions |
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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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87 if array_inputs_bigwig: |
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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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88 all_datatype_dictionary['bigwig'] = array_inputs_bigwig |
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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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89 if array_inputs_gff3_transcript: |
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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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90 all_datatype_dictionary['gff3_transcript'] = array_inputs_gff3_transcript |
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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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91 if array_inputs_gff3_mrna: |
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92 all_datatype_dictionary['gff3_mrna'] = array_inputs_gff3_mrna |
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93 if array_inputs_gtf: |
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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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94 all_datatype_dictionary['gtf'] = array_inputs_gtf |
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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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95 if array_inputs_blastxml: |
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96 all_datatype_dictionary['blastxml'] = array_inputs_blastxml |
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97 |
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98 print all_datatype_dictionary |
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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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99 |
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100 for datatype, inputfiles in all_datatype_dictionary.items(): |
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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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101 try: |
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102 if not inputfiles: |
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103 raise ValueError('empty input, must provide track files!\n') |
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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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104 except IOError: |
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105 print 'Cannot open', datatype |
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106 else: |
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107 for f in inputfiles: |
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108 all_tracks.addToRaw(f, datatype) |
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109 |
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110 jbrowseHub = TrackHub.TrackHub(all_tracks, reference, out_path, tool_directory, genome, extra_files_path) |
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111 jbrowseHub.createHub() |
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112 |
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113 |
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114 if __name__ == "__main__": |
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115 main(sys.argv) |
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116 |