Mercurial > repos > yating-l > jbrowse_hub

annotate trackObject.py @ 28:5580dbf2a31c draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit e81fecac281f299db00cfc88a068e056b031ae9d-dirty
author yating-l
date Wed, 15 Mar 2017 11:36:09 -0400
parents a4a54b925c73
children d8049deb0c97
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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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8 import tempfile
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9 import subprocess
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11 class trackObject:
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12 def __init__(self, chrom_size, genome, extra_files_path):
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13 self.chrom_size = chrom_size
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14 outputDirect = os.path.join(extra_files_path, genome)
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15 self.raw_folder = os.path.join(outputDirect, 'raw')
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16 print self.raw_folder
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17 self.tracks = []
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18 try:
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19 if os.path.exists(self.raw_folder):
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20 if os.path.isdir(self.raw_folder):
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21 shutil.rmtree(self.raw_folder)
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22 else:
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23 os.remove(self.raw_folder)
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24 os.makedirs(self.raw_folder)
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25 except OSError as oserror:
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26 print "Cannot create raw folder error({0}): {1}".format(oserror.errno, oserror.strerror)
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28 def addToRaw(self, dataFile, dataType):
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29 '''
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30 Convert gff3, BED, blastxml and gtf files into gff3 files
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31 and store converted files in folder 'raw'
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32 '''
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34 fileName = os.path.basename(dataFile)
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35 des_path = os.path.join(self.raw_folder, fileName)
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36 track = {}
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37 if dataType == 'gff3_mrna' or dataType == 'gff3_transcript' or dataType == 'fasta' or dataType == 'bam' or dataType == 'bigwig' or dataType == 'bai':
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38 if dataType == 'bam':
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39 # JBrowse will raise error: not a BAM file if the filename hasn't .bam extension
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40 fileName = os.path.basename(dataFile) + '.bam'
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41 des_path = os.path.join(self.raw_folder, fileName)
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42 bam_index = utils.createBamIndex(dataFile)
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43 indexname = os.path.basename(bam_index)
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44 des_path_for_index = os.path.join(self.raw_folder, indexname)
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45 shutil.copyfile(bam_index, des_path_for_index)
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46 track['index'] = indexname
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47
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48 try:
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49 shutil.copyfile(dataFile, des_path)
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50 except shutil.Error as err1:
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51 print "Cannot move file, error({0}: {1})".format(err1.errno, err1.strerror)
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52 except IOError as err2:
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53 print "Cannot move file, error({0}: {1})".format(err2.errno, err2.strerror)
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54 elif dataType == 'bedSimpleRepeats':
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55 bedToGff3.bedToGff3(dataFile, self.chrom_size, 'trfbig', des_path)
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56 elif dataType == 'bedSpliceJunctions':
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57 bedToGff3.bedToGff3(dataFile, self.chrom_size, 'regtools', des_path)
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58 elif dataType == 'blastxml':
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59 blastxmlToGff3.blastxml2gff3(dataFile, des_path)
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60 elif dataType == 'gtf':
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61 utils.gtfToGff3(dataFile, des_path, self.chrom_size)
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62 track['fileName'] = fileName
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63 track['dataType'] = dataType
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64 self.tracks.append(track)
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65
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68 '''
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69 def checkGff3(self, dataFile, dataType):
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70 with open(dataFile, 'r') as f:
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71 for line in f:
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72 if not line.startswith('#'):
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73 seq_type = line.rstrip().split('\t')[2]
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74 if seq_type == 'transcript':
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75 return 'gff3-transcript'
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76 if seq_type == 'mRNA':
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77 return 'gff3'
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78 '''