Mercurial > repos > yating-l > jbrowse_hub

annotate jbrowse_hub.py @ 46:66db979c21f0 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 73ede51a133dc8914812195a1b4cd512bfb8f23d-dirty
author yating-l
date Wed, 22 Mar 2017 15:17:19 -0400
parents a5108e5010b4
children 3e5b6f6a9abe
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 sys
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
4 import argparse
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
5 import json
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
6 import utils
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
7 import trackObject
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
8 import TrackHub
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
9
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
10
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
11
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
12 def main(argv):
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
13 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
14
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
15 # Reference genome mandatory
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
16 parser.add_argument('-f', '--fasta', help='Fasta file of the reference genome (Required)')
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
17
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
18 # Genome name
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
19 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
20
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
21 # Output folder
5
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('-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
23
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
24 # Output folder
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
25 parser.add_argument('-e', '--extra_files_path', help='Directory of JBrowse Hub folder')
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
26
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
27 #Tool Directory
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
28 parser.add_argument('-d', '--tool_directory', help='The directory of JBrowse file convertion scripts and UCSC tools')
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
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
48 # BIGWIG format
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
49 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
50
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
51 # GTF format
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
52 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
53
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
54 # Metadata json format
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
55 parser.add_argument('-j', '--data_json', help='Json containing the metadata of the inputs')
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
56
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
57 args = parser.parse_args()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
58 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
59
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
60
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
61 if not args.fasta:
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
62 parser.print_help()
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
63 raise RuntimeError("No reference genome\n")
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
64 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
65 genome = 'unknown'
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
66 out_path = 'unknown.html'
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
67 extra_files_path = '.'
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
68 tool_directory = '.'
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
69 if args.genome_name:
36
d5ec43607f66 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 33
diff changeset
70 genome = args.genome_name
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
71 if args.out:
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
72 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
73 if args.extra_files_path:
36
d5ec43607f66 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 33
diff changeset
74 extra_files_path = args.extra_files_path
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
75
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
76 #tool_directory not work for Galaxy tool, all tools need to exist in the current PATH, deal with it with tool dependencies
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
77 if args.tool_directory:
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
78 tool_directory = args.tool_directory
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
79
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
80 #Calculate chromsome sizes using genome reference and uscs tools
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
81 chrom_size = utils.getChromSizes(reference, tool_directory)
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
82
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
83 #get metadata from json file
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
84 json_inputs_data = args.data_json
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
85 if json_inputs_data:
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
86 inputs_data = json.loads(json_inputs_data)
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
87 else:
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
88 inputs_data = {}
33
39a214ac35a7 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 31
diff changeset
89
39a214ac35a7 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 31
diff changeset
90 #print inputs_data
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
91
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
92 #Initate trackObject
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
93 all_tracks = trackObject.trackObject(chrom_size.name, genome, extra_files_path)
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
94
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
95 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
96 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
97 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
98 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
99 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
100 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
101 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
102 array_inputs_blastxml = args.blastxml
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
103
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
104 if array_inputs_bam:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
105 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
106 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
107 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
108 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
109 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
110 if array_inputs_bigwig:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
111 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
112 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
113 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
114 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
115 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
116 if array_inputs_gtf:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
117 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
118 if array_inputs_blastxml:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
119 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
120
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
121 print "input tracks: \n", all_datatype_dictionary
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
122
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
123 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
124 try:
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 0
diff changeset
125 if not inputfiles:
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
126 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
127 except IOError:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
128 print 'Cannot open', datatype
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
129 else:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
130 for f in inputfiles:
42
a5108e5010b4 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 149c5cbda82f49f260767b5710f0c2160eebc881-dirty
yating-l
parents: 39
diff changeset
131 #metadata = {}
33
39a214ac35a7 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 31
diff changeset
132 #print f
42
a5108e5010b4 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 149c5cbda82f49f260767b5710f0c2160eebc881-dirty
yating-l
parents: 39
diff changeset
133 #if f in inputs_data.keys():
a5108e5010b4 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 149c5cbda82f49f260767b5710f0c2160eebc881-dirty
yating-l
parents: 39
diff changeset
134 # metadata = inputs_data[f]
a5108e5010b4 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 149c5cbda82f49f260767b5710f0c2160eebc881-dirty
yating-l
parents: 39
diff changeset
135 #print metadata
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
136 #Convert tracks into gff3 format
42
a5108e5010b4 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 149c5cbda82f49f260767b5710f0c2160eebc881-dirty
yating-l
parents: 39
diff changeset
137 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
138
42
a5108e5010b4 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 149c5cbda82f49f260767b5710f0c2160eebc881-dirty
yating-l
parents: 39
diff changeset
139 jbrowseHub = TrackHub.TrackHub(all_tracks, reference, out_path, tool_directory, genome, extra_files_path, inputs_data)
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
140 jbrowseHub.createHub()
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
141
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
142 """
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
143 def extractMetadata(array_inputs, inputs_data):
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
144 metadata_dict = {}
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
145 for input_false_path in array_inputs:
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
146 for key, data_value in inputs_data.items():
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
147 if key == input_false_path:
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
148 metadata_dict[input_false_path]
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 28
diff changeset
149 """
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
150
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
151 if __name__ == "__main__":
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
152 main(sys.argv)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
153