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annotate Bam.py @ 0:abcfd662b679 draft default tip

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planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
author yating-l
date Thu, 22 Dec 2016 17:53:00 -0500
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abcfd662b679 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test.git commit 199ae2b10f3b3e58cb4d4a3b9fb4b35db415c538-dirty
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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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7
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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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11
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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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15 from util import subtools
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16
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17
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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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37
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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
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41 # First: Add the bam file
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42 # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html)
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44 bam_file_path = os.path.join(self.myTrackFolderPath, self.name_bam)
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45 shutil.copyfile(self.input_bam_false_path, bam_file_path)
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46
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47 # Create and add the bam index file to the same folder
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48 name_index_bam = self.name_bam + ".bai"
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49 bam_index_file_path = os.path.join(self.myTrackFolderPath, name_index_bam)
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50 shutil.copyfile(self.index_bam, bam_index_file_path)
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51
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52 # Create the Track Object
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53 self.createTrack(file_path=self.name_bam,
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54 track_name=self.name_bam,
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55 long_label=self.name_bam, track_type='bam', visibility='pack', priority=self.priority,
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56 track_file=bam_index_file_path,
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57 track_color=self.track_color,
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58 group_name=self.group_name
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59 )
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60 #
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61 # dataURL = "tracks/%s" % self.name_bam
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62 #
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63 # trackDb = TrackDb(
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64 # trackName=self.name_bam,
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65 # longLabel=self.name_bam,
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66 # shortLabel=self.getShortName( self.name_bam ),
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67 # trackDataURL=dataURL,
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68 # trackType='bam',
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69 # visibility='pack',
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70 # priority=self.priority,
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71 # )
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72 #
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73 # # Return the Bam Track Object
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74 # self.track = Track(
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75 # trackFile=bam_index_file_path,
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76 # trackDb=trackDb,
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77 # )
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78
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79 print("- Bam %s created" % self.name_bam)
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80 #print("- %s created in %s" % (self.name_bam, bam_file_path))
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81 #print("- %s created in %s" % (self.index_bam, bam_index_file_path))