Mercurial > repos > yating-l > jbrowse_hub

annotate trackObject.py @ 40:4af741177682 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
author yating-l
date Fri, 17 Mar 2017 19:01:21 -0400
parents 75edbc203532
children a5108e5010b4
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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, metaData):
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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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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 = os.path.basename(dataFile) + '.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 self.SetMetadata(track, metaData)
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64 self.tracks.append(track)
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66 #If the metadata is not set, use the default value
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67 def SetMetadata(self, track, metaData):
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68 track.update(metaData)
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69 if 'name' not in metaData.keys() or track['name'] == '':
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70 track['name'] = track['fileName']
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71 if 'label' not in metaData.keys() or track['label'] == '':
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72 track['label'] = track['name']
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73 if 'track_color' not in metaData.keys() or track['track_color'] == '':
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74 track['track_color'] = "#daa520"
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75 if track['dataType'] == 'bigwig':
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76 if 'pos_color' not in metaData.keys() or track['pos_color'] == '':
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77 track['pos_color'] = "#FFA600"
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78 if 'neg_color' not in metaData.keys() or track['neg_color'] == '':
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79 track['neg_color'] = "#005EFF"