Mercurial > repos > yating-l > jbrowse_hub

annotate TrackHub.py @ 3:b01abbba3457 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
author yating-l
date Fri, 10 Mar 2017 14:37:16 -0500
parents e4f3f2ed4fa5
children e7c80e9b70ae
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e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
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1 #!/usr/bin/env python
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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2
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yating-l
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3 import os
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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4 import trackObject
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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5 import utils
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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6 import subprocess
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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7 import string
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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8 import shutil
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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9 from mako.lookup import TemplateLookup
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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10
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yating-l
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11 class TrackHub:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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12 def __init__(self, inputFiles, reference, outputDirect, tool_dir):
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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13 self.input_files = inputFiles
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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14 self.out_path = outputDirect
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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15 self.reference = reference
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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16 self.tool_dir = tool_dir
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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17 try:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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18 if not self.out_path:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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19 raise ValueError('empty output path\n')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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20 if os.path.exists(self.out_path):
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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21 shutil.rmtree(self.out_path)
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yating-l
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22 os.mkdir(self.out_path)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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23 self.json = os.path.join(self.out_path, 'json')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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24 if os.path.exists(self.json):
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yating-l
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25 shutil.rmtree(self.json)
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yating-l
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26 os.mkdir(self.json)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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27 self.raw = os.path.join(self.out_path, 'raw')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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28 if os.path.exists(self.raw):
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yating-l
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29 shutil.rmtree(self.raw)
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yating-l
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30 shutil.move('raw', self.out_path)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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31 except OSError as e:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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32 print "Cannot create json folder error({0}): {1}".format(e.errno, e.strerror)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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33 else:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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34 print "Create jbrowse folder {}".format(self.out_path)
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yating-l
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35
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yating-l
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36 def createHub(self):
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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37 self.prepareRefseq()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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38 for input_file in self.input_files:
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yating-l
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39 self.addTrack(input_file)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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40 self.indexName()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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41 self.makeArchive()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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42 shutil.rmtree(self.out_path)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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43 print "Success!\n"
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44
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45 def prepareRefseq(self):
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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46 try:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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47 p = subprocess.Popen([os.path.join(self.tool_dir, 'prepare-refseqs.pl'), '--fasta', self.reference, '--out', self.json])
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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48 # Wait for process to terminate.
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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49 p.communicate()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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50 except OSError as e:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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51 print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror)
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52
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yating-l
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53 def addTrack(self, track):
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yating-l
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54 if track.dataType == 'bam':
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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55 json_file = os.path.join(self.json, "trackList.json")
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yating-l
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56 bam_track = dict()
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yating-l
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57 bam_track['type'] = 'JBrowse/View/Track/Alignments2'
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yating-l
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58 bam_track['label'] = track.fileName
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yating-l
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59 bam_track['urlTemplate'] = os.path.join('../raw', track.fileName)
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yating-l
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60 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks')
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yating-l
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61 print "add bam track\n"
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yating-l
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62 elif track.dataType == 'bigwig':
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yating-l
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63 json_file = os.path.join(self.json, "trackList.json")
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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64 bigwig_track = dict()
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yating-l
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65 bigwig_track['label'] = 'rnaseq'
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yating-l
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66 bigwig_track['key'] = 'RNA-Seq Coverage'
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yating-l
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67 bigwig_track['urlTemplate'] = os.path.join('../raw', track.fileName)
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yating-l
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68 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
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yating-l
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69 bigwig_track['variance_band'] = True
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yating-l
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70 bigwig_track['style'] = dict()
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71 bigwig_track['style']['pos_color'] = '#FFA600'
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yating-l
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72 bigwig_track['style']['neg_color'] = '#005EFF'
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yating-l
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73 bigwig_track['style']['clip_marker_color'] = 'red'
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yating-l
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74 bigwig_track['style']['height'] = 100
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yating-l
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75 utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks')
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76 else:
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yating-l
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77 gff3_file = os.path.join(self.raw, track.fileName)
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yating-l
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78 label = track.fileName
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yating-l
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79 if track.dataType == 'bedSpliceJunctions' or track.dataType == 'gtf':
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yating-l
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80 p = subprocess.Popen([os.path.join(self.tool_dir, 'flatfile-to-json.pl'), '--gff', gff3_file, '--trackType', 'CanvasFeatures', '--trackLabel', label, '--config', '{"glyph": "JBrowse/View/FeatureGlyph/Segments"}', '--out', self.json])
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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81 elif track.dataType == 'gff3-transcript':
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yating-l
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82 p = subprocess.Popen([os.path.join(self.tool_dir, 'flatfile-to-json.pl'), '--gff', gff3_file, '--trackType', 'MyPlugin/GenePred', '--trackLabel', label, '--config', '{"transcriptType": "transcript"}', '--out', self.json])
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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83 elif track.dataType == 'gff3':
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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84 p = subprocess.Popen([os.path.join(self.tool_dir, 'flatfile-to-json.pl'), '--gff', gff3_file, '--trackType', 'MyPlugin/GenePred', '--trackLabel', label, '--out', self.json])
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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85 else:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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86 p = subprocess.Popen([os.path.join(self.tool_dir, 'flatfile-to-json.pl'), '--gff', gff3_file, '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', self.json])
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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87 p.communicate()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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88
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yating-l
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89 def indexName(self):
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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90 p = subprocess.Popen([os.path.join(self.tool_dir, 'generate-names.pl'), '-v', '--out', self.json])
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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91 p.communicate()
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92 print "finished name index \n"
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94 def makeArchive(self):
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95 filename = os.path.basename(self.out_path)
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96 shutil.make_archive(filename, 'tar', self.out_path)
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