Mercurial > repos > yating-l > jbrowse_hub

annotate trackObject.py @ 5:e7c80e9b70ae draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
author yating-l
date Tue, 14 Mar 2017 12:24:37 -0400
parents e4f3f2ed4fa5
children e1f188b43750
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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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9 class trackObject:
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10 def __init__(self, chrom_size, genome, extra_files_path):
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11 self.chrom_size = chrom_size
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12 outputDirect = os.path.join(extra_files_path, genome)
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13 self.raw_folder = os.path.join(outputDirect, 'raw')
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14 print self.raw_folder
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15 self.tracks = []
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16 try:
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17 if os.path.exists(self.raw_folder):
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18 if os.path.isdir(self.raw_folder):
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19 shutil.rmtree(self.raw_folder)
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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20 else:
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21 os.remove(self.raw_folder)
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22 os.makedirs(self.raw_folder)
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23 except OSError as oserror:
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24 print "Cannot create raw folder error({0}): {1}".format(oserror.errno, oserror.strerror)
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25
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26 def addToRaw(self, dataFile, dataType):
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27 '''
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28 Convert gff3, BED, blastxml and gtf files into gff3 files
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29 and store converted files in folder 'raw'
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30 '''
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31 fileName = os.path.basename(dataFile)
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32 des_path = os.path.join(self.raw_folder, fileName)
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33 if dataType == 'gff3' or dataType == 'fasta' or dataType == 'bam' or dataType == 'bigwig' or dataType == 'bai':
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34 if dataType == 'gff3':
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35 self.checkGff3(dataFile)
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36 try:
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37 shutil.copyfile(dataFile, des_path)
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38 except shutil.Error as err1:
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39 print "Cannot move file, error({0}: {1})".format(err1.errno, err1.strerror)
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40 except IOError as err2:
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41 print "Cannot move file, error({0}: {1})".format(err2.errno, err2.strerror)
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42 elif dataType == 'bedSimpleRepeats':
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43 bedToGff3.bedToGff3(dataFile, self.chrom_size, 'trfbig', des_path)
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44 elif dataType == 'bedSpliceJunctions':
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45 bedToGff3.bedToGff3(dataFile, self.chrom_size, 'regtools', des_path)
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46 elif dataType == 'blastxml':
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47 blastxmlToGff3.blastxml2gff3(dataFile, des_path)
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48 elif dataType == 'gtf':
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49 utils.gtfToGff3(dataFile, des_path, self.chrom_size)
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50 track = {
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51 'fileName': fileName,
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52 'dataType': dataType
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53 }
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54 self.tracks.append(track)
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55
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56 def checkGff3(self, dataFile):
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57 with open(dataFile, 'r') as f:
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58 for line in f:
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59 if not line.startswith('#'):
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60 seq_type = line.rstrip().split('\t')[2]
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61 if seq_type == 'transcript':
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62 dataType = 'gff3-transcript'
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63 break
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64 if seq_type == 'mRNA':
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65 break