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annotate Bam.py @ 26:df42241d3731 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
author yating-l
date Mon, 03 Jul 2017 17:30:20 -0400
parents 2677f1899aa8
children
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rmarenco
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1 #!/usr/bin/python
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rmarenco
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2 # -*- coding: utf8 -*-
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4 """
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rmarenco
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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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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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rmarenco
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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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32
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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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yating-l
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40 self.database = self.data_bam["database"]
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41 if self.data_bam["long_label"]:
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42 self.long_label = self.data_bam["long_label"]
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43 else:
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44 self.long_label = self.name_bam
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45 # First: Add the bam file
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46 # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html)
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48 bam_file_path = os.path.join(self.myTrackFolderPath, self.name_bam)
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49 shutil.copyfile(self.input_bam_false_path, bam_file_path)
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51 # Create and add the bam index file to the same folder
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52 name_index_bam = self.name_bam + ".bai"
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53 bam_index_file_path = os.path.join(self.myTrackFolderPath, name_index_bam)
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54 shutil.copyfile(self.index_bam, bam_index_file_path)
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56 # Create the Track Object
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57 self.createTrack(file_path=self.name_bam,
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58 track_name=self.name_bam,
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yating-l
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59 long_label=self.long_label, track_type='bam', visibility='pack', priority=self.priority,
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60 track_file=bam_index_file_path,
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61 track_color=self.track_color,
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62 group_name=self.group_name,
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63 database=self.database
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64 )
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65 #
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66 # dataURL = "tracks/%s" % self.name_bam
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67 #
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68 # trackDb = TrackDb(
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69 # trackName=self.name_bam,
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70 # longLabel=self.name_bam,
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71 # shortLabel=self.getShortName( self.name_bam ),
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72 # trackDataURL=dataURL,
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73 # trackType='bam',
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74 # visibility='pack',
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75 # priority=self.priority,
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76 # )
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77 #
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78 # # Return the Bam Track Object
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79 # self.track = Track(
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80 # trackFile=bam_index_file_path,
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81 # trackDb=trackDb,
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82 # )
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83
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84 print("- Bam %s created" % self.name_bam)
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85 #print("- %s created in %s" % (self.name_bam, bam_file_path))
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86 #print("- %s created in %s" % (self.index_bam, bam_index_file_path))