Mercurial > repos > yating-l > jbrowse_hub

annotate jbrowse_hub.py @ 12:e1f188b43750 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
author yating-l
date Tue, 14 Mar 2017 14:31:36 -0400
parents e7c80e9b70ae
children f2285f29a6fa
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
1 #!/usr/bin/env python
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
2
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
3 import os
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
4 import sys
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
5 import argparse
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
6 import subprocess
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
7 from bedToGff3 import bedToGff3
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
8 import blastxmlToGff3
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
9 import utils
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
10 import tempfile
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
11 import trackObject
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
12 import TrackHub
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
13 import shutil
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
14
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
15 def main(argv):
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
16 parser = argparse.ArgumentParser(description='Create a hub to display in jbrowse.')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
17
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
18 # Reference genome mandatory
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
19 parser.add_argument('-f', '--fasta', help='Fasta file of the reference genome')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
20
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
21 # Genome name
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
22 parser.add_argument('-g', '--genome_name', help='Name of reference genome')
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
23
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
24 # Output folder
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
25 parser.add_argument('-o', '--out', help='output html')
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
26
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
27 # Output folder
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
28 parser.add_argument('-e', '--extra_files_path', help="Directory of JBrowse Hub folder")
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
29
12
e1f188b43750 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 5
diff changeset
30 # GFF3 structure: gene->transcription->CDS
e1f188b43750 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 5
diff changeset
31 parser.add_argument('--gff3_transcript', action='append', help='GFF3 format, structure: gene->transcription->CDS')
e1f188b43750 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 5
diff changeset
32
e1f188b43750 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 5
diff changeset
33 # GFF3 structure: gene->mRNA->CDS
e1f188b43750 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 5
diff changeset
34 parser.add_argument('--gff3_mrna', action='append', help='GFF3 format, structure: gene->mRNA->CDS')
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
35
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
36 # trfBig simple repeats (BED 4+12)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
37 parser.add_argument('--bedSimpleRepeats', action='append', help='BED 4+12 format, using simpleRepeats.as')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
38
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
39 # regtools (BED 12+1)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
40 parser.add_argument('--bedSpliceJunctions', action='append', help='BED 12+1 format, using spliceJunctions.as')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
41
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
42 # tblastn alignment (blastxml)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
43 parser.add_argument('--blastxml', action='append', help='blastxml format from tblastn')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
44
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
45 # BAM format
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
46 parser.add_argument('--bam', action='append', help='BAM format from HISAT')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
47 # put bam index file at the same directory with bam file
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
48 # parser.add_argument('--bai', action='append', help='BAM index format from HISAT')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
49
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
50 # BIGWIG format
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
51 parser.add_argument('--bigwig', action='append', help='BIGWIG format to show rnaseq coverage')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
52
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
53 # GTF format
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
54 parser.add_argument('--gtf', action='append', help='GTF format from StringTie')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
55
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
56 args = parser.parse_args()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
57 all_datatype_dictionary = dict()
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
58
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
59
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
60 reference = args.fasta
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
61 genome = 'unknown'
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
62 out_path = '.'
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
63 extra_files_path = '.'
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
64 if args.genome_name:
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
65 genome = utils.sanitize_name_path(args.genome_name)
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
66 if args.out:
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
67 out_path = args.out
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
68 if args.extra_files_path:
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
69 extra_files_path = utils.sanitize_name_path(args.extra_files_path)
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
70 cwd = os.getcwd()
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
71 #tool_directory not work for Galaxy tool, all tools need to exist in the current PATH, deal with it with tool dependencies
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
72 tool_directory = os.path.join(cwd, 'JBrowse-1.12.1/bin')
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
73 chrom_size = utils.getChromSizes(reference, tool_directory)
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
74 all_tracks = trackObject.trackObject(chrom_size.name, genome, extra_files_path) #store converted files in the array: all_tracks.tracks
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
75 array_inputs_bam = args.bam
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
76 array_inputs_bed_simple_repeats = args.bedSimpleRepeats
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
77 array_inputs_bed_splice_junctions = args.bedSpliceJunctions
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
78 array_inputs_bigwig = args.bigwig
12
e1f188b43750 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 5
diff changeset
79 array_inputs_gff3_transcript = args.gff3_transcript
e1f188b43750 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 5
diff changeset
80 array_inputs_gff3_mrna = args.gff3_mrna
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
81 array_inputs_gtf = args.gtf
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
82 array_inputs_blastxml = args.blastxml
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
83 if array_inputs_bam:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
84 all_datatype_dictionary['bam'] = array_inputs_bam
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
85 if array_inputs_bed_simple_repeats:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
86 all_datatype_dictionary['bedSimpleRepeats'] = array_inputs_bed_simple_repeats
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
87 if array_inputs_bed_splice_junctions:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
88 all_datatype_dictionary['bedSpliceJunctions'] = array_inputs_bed_splice_junctions
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
89 if array_inputs_bigwig:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
90 all_datatype_dictionary['bigwig'] = array_inputs_bigwig
12
e1f188b43750 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 5
diff changeset
91 if array_inputs_gff3_transcript:
e1f188b43750 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 5
diff changeset
92 all_datatype_dictionary['gff3_transcript'] = array_inputs_gff3_transcript
e1f188b43750 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 5
diff changeset
93 if array_inputs_gff3_mrna:
e1f188b43750 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 5
diff changeset
94 all_datatype_dictionary['gff3_mrna'] = array_inputs_gff3_mrna
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
95 if array_inputs_gtf:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
96 all_datatype_dictionary['gtf'] = array_inputs_gtf
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
97 if array_inputs_blastxml:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
98 all_datatype_dictionary['blastxml'] = array_inputs_blastxml
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
99
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
100 print all_datatype_dictionary
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
101
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
102 for datatype, inputfiles in all_datatype_dictionary.items():
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
103 try:
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
104 if not inputfiles:
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
105 raise ValueError('empty input, must provide track files!\n')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
106 except IOError:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
107 print 'Cannot open', datatype
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
108 else:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
109 for f in inputfiles:
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
110 all_tracks.addToRaw(f, datatype)
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
111
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
112 jbrowseHub = TrackHub.TrackHub(all_tracks, reference, out_path, tool_directory, genome, extra_files_path)
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
113 jbrowseHub.createHub()
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
114
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
115
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
116
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
117 '''
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
118 if reference:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
119 p = subprocess.Popen(['JBrowse-1.12.1/bin/prepare-refseqs.pl', '--fasta', reference, '--out', out_path])
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
120 # Wait for process to terminate.
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
121 p.communicate()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
122 else:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
123 parser.print_help()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
124
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
125
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
126 if input_simple_repeats:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
127 bedToGff3(input_simple_repeats, chrom_size, 'trfbig', 'repeats.gff3')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
128 label = "repeats"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
129 p = subprocess.Popen(['JBrowse-1.12.1/bin/flatfile-to-json.pl', '--gff', 'repeats.gff3', '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', out_path])
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
130 p.communicate()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
131 if input_splice_junctions:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
132 bedToGff3(input_splice_junctions, chrom_size, 'regtools', 'regtools.gff3')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
133 label = "regtools"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
134 p = subprocess.Popen(['JBrowse-1.12.1/bin/flatfile-to-json.pl', '--gff', 'regtools.gff3', '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', out_path])
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
135 p.communicate()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
136 attr = dict()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
137 track = dict()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
138 attr['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
139 track['regtools'] = attr
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
140 json_file = os.path.join(out_path, "trackList.json")
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
141 utils.add_tracks_to_json(json_file, track, 'add_attr')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
142 if blastxml:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
143 blastxmlToGff3.blastxml2gff3(blastxml, "blast.gff3")
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
144 label = "blast"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
145 p = subprocess.Popen(['JBrowse-1.12.1/bin/flatfile-to-json.pl', '--gff', 'blast.gff3', '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', out_path])
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
146 p.communicate()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
147 if array_inputs_gff3:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
148 for gff3 in array_inputs_gff3:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
149 label = os.path.basename(gff3)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
150 label = label.replace('.', '_')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
151 p = subprocess.Popen(['JBrowse-1.12.1/bin/flatfile-to-json.pl', '--gff', gff3, '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', out_path])
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
152 p.communicate()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
153 if 'Augustus' in label:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
154 attr = dict()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
155 track = dict()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
156 attr['transcriptType'] = 'transcript'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
157 track['Augustus'] = attr
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
158 json_file = os.path.join(out_path, "trackList.json")
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
159 utils.add_tracks_to_json(json_file, track, 'add_attr')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
160 if bam:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
161 json_file = os.path.join(out_path, "trackList.json")
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
162 bam_track = dict()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
163 bam_track['type'] = 'JBrowse/View/Track/Alignments2'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
164 bam_track['label'] = 'alignments'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
165 bam_track['urlTemplate'] = '../raw/HISAT_on_data_3,_data_2,_and_data_1.bam'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
166 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
167 print "add bam track\n"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
168 if bigwig:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
169 json_file = os.path.join(out_path, "trackList.json")
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
170 bigwig_track = dict()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
171 bigwig_track['label'] = 'rnaseq'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
172 bigwig_track['key'] = 'RNA-Seq Coverage'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
173 bigwig_track['urlTemplate'] = '../raw/Convert_Bam_to_BigWig_on_data_3_and_data_15.bigwig'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
174 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
175 bigwig_track['variance_band'] = True
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
176 bigwig_track['style'] = dict()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
177 bigwig_track['style']['pos_color'] = '#FFA600'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
178 bigwig_track['style']['neg_color'] = '#005EFF'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
179 bigwig_track['style']['clip_marker_color'] = 'red'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
180 bigwig_track['style']['height'] = 100
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
181 utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
182
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
183 if gtf:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
184 utils.gtfToGff3(gtf, 'stringtie.gff3', chrom_size)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
185 label = os.path.basename('stringtie')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
186 p = subprocess.Popen(['JBrowse-1.12.1/bin/flatfile-to-json.pl', '--gff', 'stringtie.gff3', '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', out_path])
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
187 p.communicate()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
188 attr = dict()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
189 track = dict()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
190 attr['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
191 track['stringtie'] = attr
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
192 json_file = os.path.join(out_path, "trackList.json")
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
193 utils.add_tracks_to_json(json_file, track, 'add_attr')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
194
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
195 # Index name, it takes a long time, exclude it for now
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
196 p = subprocess.Popen(['JBrowse-1.12.1/bin/generate-names.pl', '-v', '--out', out_path])
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
197 p.communicate()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
198 print "finished name index \n"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
199 '''
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
200
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
201 if __name__ == "__main__":
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
202 main(sys.argv)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
203