Mercurial > repos > yating-l > jbrowse_hub

annotate trackObject.py @ 3:b01abbba3457 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
author yating-l
date Fri, 10 Mar 2017 14:37:16 -0500
parents e4f3f2ed4fa5
children e7c80e9b70ae
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e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
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1 #!/usr/bin/env python
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2
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3 import os
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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4 import shutil
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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5 import utils
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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6 import bedToGff3
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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7 import blastxmlToGff3
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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8
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9 class trackObject:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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10 def __init__(self, dataFile, dataType, chrom_size):
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11 self.dataFile = dataFile
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12 self.fileName = os.path.basename(dataFile)
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13 self.dataType = dataType
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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14 self.chrom_size = chrom_size
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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15 try:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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16 if not os.path.exists('raw'):
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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17 os.mkdir('raw')
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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18 except OSError as oserror:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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19 print "Cannot create raw folder error({0}): {1}".format(oserror.errno, oserror.strerror)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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20 else:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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21 self.raw_folder = 'raw'
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22
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23 def addToRaw(self):
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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24 des_path = os.path.join(self.raw_folder, self.fileName)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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25 if self.dataType == 'gff3' or self.dataType == 'fasta' or self.dataType == 'bam' or self.dataType == 'bigwig' or self.dataType == 'bai':
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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26 if self.dataType == 'gff3':
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27 self.checkGff3()
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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28 try:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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29 shutil.copyfile(self.dataFile, des_path)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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30 except shutil.Error as err1:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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31 print "Cannot move file, error({0}: {1})".format(err1.errno, err1.strerror)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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32 except IOError as err2:
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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33 print "Cannot move file, error({0}: {1})".format(err2.errno, err2.strerror)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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34 elif self.dataType == 'bedSimpleRepeats':
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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35 bedToGff3.bedToGff3(self.dataFile, self.chrom_size, 'trfbig', des_path)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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36 elif self.dataType == 'bedSpliceJunctions':
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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37 bedToGff3.bedToGff3(self.dataFile, self.chrom_size, 'regtools', des_path)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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38 elif self.dataType == 'blastxml':
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39 blastxmlToGff3.blastxml2gff3(self.dataFile, des_path)
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
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40 elif self.dataType == 'gtf':
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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41 utils.gtfToGff3(self.dataFile, des_path, self.chrom_size)
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42
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43 def checkGff3(self):
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44 with open(self.dataFile, 'r') as f:
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45 for line in f:
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46 if not line.startswith('#'):
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
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47 seq_type = line.rstrip().split('\t')[2]
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48 if seq_type == 'transcript':
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49 self.dataType = 'gff3-transcript'
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50 break
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51 if seq_type == 'mRNA':
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52 break