Mercurial > repos > yating-l > jbrowse_hub

annotate trackObject.py @ 42:a5108e5010b4 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 149c5cbda82f49f260767b5710f0c2160eebc881-dirty
author yating-l
date Mon, 20 Mar 2017 12:35:33 -0400
parents 4af741177682
children 3e5b6f6a9abe
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1 #!/usr/bin/env python
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3 import os
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4 import shutil
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5 import utils
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6 import bedToGff3
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7 import blastxmlToGff3
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10 class trackObject:
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11 def __init__(self, chrom_size, genome, extra_files_path):
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12 self.chrom_size = chrom_size
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13 outputDirect = os.path.join(extra_files_path, genome)
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14 self.raw_folder = os.path.join(outputDirect, 'raw')
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15 #Store metadata of the tracks
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16 self.tracks = []
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17 try:
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18 if os.path.exists(self.raw_folder):
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19 if os.path.isdir(self.raw_folder):
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20 shutil.rmtree(self.raw_folder)
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21 else:
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22 os.remove(self.raw_folder)
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23 os.makedirs(self.raw_folder)
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24 except OSError as oserror:
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25 print "Cannot create raw folder error({0}): {1}".format(oserror.errno, oserror.strerror)
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27 def addToRaw(self, dataFile, dataType):
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28 """
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29 Convert gff3, BED, blastxml and gtf files into gff3 files
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30 and store converted files in folder 'raw'
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31 """
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32 false_path = os.path.abspath(dataFile)
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33 fileName = os.path.basename(dataFile)
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34 des_path = os.path.join(self.raw_folder, fileName)
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35 track = {}
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36 if dataType == 'gff3_mrna' or dataType == 'gff3_transcript' or dataType == 'fasta' or dataType == 'bam' or dataType == 'bigwig' or dataType == 'bai':
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37 if dataType == 'bam':
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38 # JBrowse will raise error: not a BAM file if the filename hasn't .bam extension
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39 fileName = fileName + '.bam'
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40 des_path = os.path.join(self.raw_folder, fileName)
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41 bam_index = utils.createBamIndex(dataFile)
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42 indexname = os.path.basename(bam_index)
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43 des_path_for_index = os.path.join(self.raw_folder, indexname)
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44 shutil.copyfile(bam_index, des_path_for_index)
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45 track['index'] = indexname
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47 try:
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48 shutil.copyfile(dataFile, des_path)
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49 except shutil.Error as err1:
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50 print "Cannot move file, error({0}: {1})".format(err1.errno, err1.strerror)
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51 except IOError as err2:
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52 print "Cannot move file, error({0}: {1})".format(err2.errno, err2.strerror)
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53 elif dataType == 'bedSimpleRepeats':
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54 bedToGff3.bedToGff3(dataFile, self.chrom_size, 'trfbig', des_path)
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55 elif dataType == 'bedSpliceJunctions':
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56 bedToGff3.bedToGff3(dataFile, self.chrom_size, 'regtools', des_path)
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57 elif dataType == 'blastxml':
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58 blastxmlToGff3.blastxml2gff3(dataFile, des_path)
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59 elif dataType == 'gtf':
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60 utils.gtfToGff3(dataFile, des_path, self.chrom_size)
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61 track['fileName'] = fileName
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62 track['dataType'] = dataType
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63 track['false_path'] = false_path
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64 #self.SetMetadata(track, metaData)
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65 self.tracks.append(track)
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