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annotate Bam.py @ 55:ba9997c847dc draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
author yating-l
date Wed, 17 May 2017 13:16:57 -0400
parents c66803bff0cc
children b39dd0b5a166
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1 #!/usr/bin/python
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2 # -*- coding: utf8 -*-
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3
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4 """
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5 Class to handle Bam files to UCSC TrackHub
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6 """
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8 import logging
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9 import os
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10 import shutil
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12 from Datatype import Datatype
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13 from Track import Track
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14 from TrackDb import TrackDb
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18 class Bam( Datatype ):
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19 def __init__(self, input_bam_false_path, data_bam):
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20 super(Bam, self).__init__()
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22 self.track = None
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24 self.input_bam_false_path = input_bam_false_path
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25
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26 self.data_bam = data_bam
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27 # TODO: Check if it already contains the .bam extension / Do a function in Datatype which check the extension
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28 if ".bam" not in self.data_bam["name"]:
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29 self.name_bam = self.data_bam["name"] + ".bam"
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30 else:
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31 self.name_bam = self.data_bam["name"]
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33 self.priority = self.data_bam["order_index"]
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34 self.index_bam = self.data_bam["index"]
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35 # TODO: Think about how to avoid repetition of the color treatment
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36 self.track_color = self.data_bam["track_color"]
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38 # TODO: Think about how to avoid repetition of the group_name everywhere
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39 self.group_name = self.data_bam["group_name"]
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40 if self.data_bam["long_label"]:
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41 self.long_label = self.data_bam["long_label"]
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42 else:
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43 self.long_label = self.name_bam
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44 # First: Add the bam file
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45 # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html)
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47 bam_file_path = os.path.join(self.myTrackFolderPath, self.name_bam)
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48 shutil.copyfile(self.input_bam_false_path, bam_file_path)
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49
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50 # Create and add the bam index file to the same folder
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51 name_index_bam = self.name_bam + ".bai"
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52 bam_index_file_path = os.path.join(self.myTrackFolderPath, name_index_bam)
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53 shutil.copyfile(self.index_bam, bam_index_file_path)
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54
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55 # Create the Track Object
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56 self.createTrack(file_path=self.name_bam,
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57 track_name=self.name_bam,
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58 long_label=self.long_label, track_type='bam', visibility='pack', priority=self.priority,
0
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59 track_file=bam_index_file_path,
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60 track_color=self.track_color,
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61 group_name=self.group_name
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62 )
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63 #
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64 # dataURL = "tracks/%s" % self.name_bam
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65 #
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66 # trackDb = TrackDb(
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67 # trackName=self.name_bam,
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68 # longLabel=self.name_bam,
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69 # shortLabel=self.getShortName( self.name_bam ),
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70 # trackDataURL=dataURL,
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71 # trackType='bam',
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72 # visibility='pack',
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73 # priority=self.priority,
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74 # )
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75 #
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76 # # Return the Bam Track Object
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77 # self.track = Track(
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78 # trackFile=bam_index_file_path,
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79 # trackDb=trackDb,
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80 # )
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81
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82 print("- Bam %s created" % self.name_bam)
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83 #print("- %s created in %s" % (self.name_bam, bam_file_path))
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84 #print("- %s created in %s" % (self.index_bam, bam_index_file_path))