Mercurial > repos > yating-l > jbrowsearchivecreator
comparison datatypes/Datatype.py @ 46:061da5d3a219 draft
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 3160592f4119e684ab5843dd28a2e6cf11df0121-dirty
| author | yating-l |
|---|---|
| date | Tue, 19 Jun 2018 16:28:36 -0400 |
| parents | 4a69515eed63 |
| children | 1eb4adefd747 |
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| 45:d56955fc4c75 | 46:061da5d3a219 |
|---|---|
| 47 self.dataType = None | 47 self.dataType = None |
| 48 self.trackFileType = None | 48 self.trackFileType = None |
| 49 self.track = None | 49 self.track = None |
| 50 self.trackSettings = dict() | 50 self.trackSettings = dict() |
| 51 self.extraSettings = collections.OrderedDict() | 51 self.extraSettings = collections.OrderedDict() |
| 52 self.nameIndex = False | |
| 52 | 53 |
| 53 | 54 |
| 54 @staticmethod | 55 @staticmethod |
| 55 def pre_init(reference_genome, chrom_sizes_file, | 56 def pre_init(reference_genome, chrom_sizes_file, |
| 56 extra_files_path, tool_directory, specie_folder, tracks_folder, binary_folder, track_type): | 57 extra_files_path, tool_directory, specie_folder, tracks_folder, binary_folder, track_type): |
| 96 self.trackType = self.trackSettings["trackType"] | 97 self.trackType = self.trackSettings["trackType"] |
| 97 if self.trackSettings["group_name"]: | 98 if self.trackSettings["group_name"]: |
| 98 self.extraSettings["category"] = self.trackSettings["group_name"] | 99 self.extraSettings["category"] = self.trackSettings["group_name"] |
| 99 if "track_color" in self.trackSettings and self.trackSettings["track_color"]: | 100 if "track_color" in self.trackSettings and self.trackSettings["track_color"]: |
| 100 self.extraSettings["color"] = self.trackSettings["track_color"] | 101 self.extraSettings["color"] = self.trackSettings["track_color"] |
| 102 #store information of whether to generate name index for the track | |
| 103 self.extraSettings["nameIndex"] = self.trackSettings["nameIndex"] | |
| 101 | 104 |
| 102 | 105 |
| 103 @abc.abstractmethod | 106 @abc.abstractmethod |
| 104 def createTrack(self): | 107 def createTrack(self): |
| 105 """Create the final track file""" | 108 """Create the final track file""" |