Mercurial > repos > yating-l > jbrowse_hub

annotate jbrowse_hub.py @ 28:5580dbf2a31c draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit e81fecac281f299db00cfc88a068e056b031ae9d-dirty
author yating-l
date Wed, 15 Mar 2017 11:36:09 -0400
parents a4a54b925c73
children d8049deb0c97
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1 #!/usr/bin/env python
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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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15 def main(argv):
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16 parser = argparse.ArgumentParser(description='Create a hub to display in jbrowse.')
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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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21 # Genome name
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22 parser.add_argument('-g', '--genome_name', help='Name of reference genome')
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24 # Output folder
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25 parser.add_argument('-o', '--out', help='output html')
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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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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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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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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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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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42 # tblastn alignment (blastxml)
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43 parser.add_argument('--blastxml', action='append', help='blastxml format from tblastn')
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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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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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51 # GTF format
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52 parser.add_argument('--gtf', action='append', help='GTF format from StringTie')
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54 args = parser.parse_args()
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55 all_datatype_dictionary = dict()
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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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87 if array_inputs_bigwig:
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88 all_datatype_dictionary['bigwig'] = array_inputs_bigwig
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89 if array_inputs_gff3_transcript:
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90 all_datatype_dictionary['gff3_transcript'] = array_inputs_gff3_transcript
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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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94 all_datatype_dictionary['gtf'] = array_inputs_gtf
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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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99
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100 for datatype, inputfiles in all_datatype_dictionary.items():
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101 try:
5
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102 if not inputfiles:
0
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103 raise ValueError('empty input, must provide track files!\n')
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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:
5
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108 all_tracks.addToRaw(f, datatype)
0
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109
5
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110 jbrowseHub = TrackHub.TrackHub(all_tracks, reference, out_path, tool_directory, genome, extra_files_path)
0
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111 jbrowseHub.createHub()
5
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112
0
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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