Mercurial > repos > yating-l > jbrowsearchivecreator

annotate trackObject.py @ 0:804a93e87cc8 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
author yating-l
date Wed, 12 Apr 2017 17:41:55 -0400
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children 7e471cdd9e71
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804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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1 #!/usr/bin/env python
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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3 import os
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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4 import shutil
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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5 import utils
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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6 import bedToGff3
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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7 import blastxmlToGff3
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
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8
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804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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10 class trackObject:
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
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11 def __init__(self, chrom_size, genome, extra_files_path):
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12 self.chrom_size = chrom_size
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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13 outputDirect = os.path.join(extra_files_path, genome)
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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14 self.raw_folder = os.path.join(outputDirect, 'raw')
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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15 #Store metadata of the tracks
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
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16 self.tracks = []
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
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17 try:
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
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18 if os.path.exists(self.raw_folder):
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yating-l
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19 if os.path.isdir(self.raw_folder):
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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20 shutil.rmtree(self.raw_folder)
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
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21 else:
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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22 os.remove(self.raw_folder)
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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23 os.makedirs(self.raw_folder)
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
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24 except OSError as oserror:
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
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25 print "Cannot create raw folder error({0}): {1}".format(oserror.errno, oserror.strerror)
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
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27 def addToRaw(self, dataFile, dataType):
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28 """
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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29 Convert gff3, BED, blastxml and gtf files into gff3 files
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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30 and store converted files in folder 'raw'
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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31 """
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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32 false_path = os.path.abspath(dataFile)
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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33 fileName = os.path.basename(dataFile)
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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34 des_path = os.path.join(self.raw_folder, fileName)
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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35 track = {}
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
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36 if dataType == 'bed' or dataType == 'gff3' or dataType == 'gff3_mrna' or dataType == 'gff3_transcript' or dataType == 'fasta' or dataType == 'bam' or dataType == 'bigwig':
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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37 if dataType == 'bam':
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
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38 # JBrowse will raise error: not a BAM file if the filename hasn't .bam extension
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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39 extension = os.path.splitext(fileName)[1]
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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40 if extension != '.bam':
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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41 fileName = fileName + '.bam'
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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42 des_path = os.path.join(self.raw_folder, fileName)
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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43 bam_index = utils.createBamIndex(dataFile)
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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44 indexname = os.path.basename(bam_index)
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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45 des_path_for_index = os.path.join(self.raw_folder, indexname)
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
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46 shutil.copyfile(bam_index, des_path_for_index)
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47 track['index'] = indexname
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49 try:
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
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50 shutil.copyfile(dataFile, des_path)
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yating-l
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51 except shutil.Error as err1:
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52 print "Cannot move file, error({0}: {1})".format(err1.errno, err1.strerror)
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53 except IOError as err2:
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54 print "Cannot move file, error({0}: {1})".format(err2.errno, err2.strerror)
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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55 elif dataType == 'bedSimpleRepeats':
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56 bedToGff3.bedToGff3(dataFile, self.chrom_size, 'trfbig', des_path)
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
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57 elif dataType == 'bedSpliceJunctions':
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yating-l
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58 bedToGff3.bedToGff3(dataFile, self.chrom_size, 'regtools', des_path)
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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59 elif dataType == 'blastxml':
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yating-l
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60 blastxmlToGff3.blastxml2gff3(dataFile, des_path)
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61 elif dataType == 'gtf':
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62 utils.gtfToGff3(dataFile, des_path, self.chrom_size)
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63 track['fileName'] = fileName
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yating-l
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64 track['dataType'] = dataType
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65 track['false_path'] = false_path
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yating-l
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66 #self.SetMetadata(track, metaData)
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67 self.tracks.append(track)
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