Mercurial > repos > yating-l > jbrowsearchivecreator

annotate bedToGff3.py @ 0:804a93e87cc8 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
author yating-l
date Wed, 12 Apr 2017 17:41:55 -0400
parents
children 7e471cdd9e71
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0
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
parents:
diff changeset
1 #!/usr/bin/env python
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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2
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yating-l
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3 '''
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yating-l
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4 Convert BED format to gff3
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yating-l
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5 '''
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yating-l
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6 import os
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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7 from collections import OrderedDict
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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8 import utils
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9
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yating-l
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10 class bedToGff3():
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yating-l
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11 def __init__(self, inputBedFile, chrom_sizes, bed_type, output):
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12 self.input = inputBedFile
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yating-l
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13 #file_dir = os.path.basename(inputBedFile)
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yating-l
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14 #print file_dir + "\n\n"
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15 self.output = output
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16 self.chrom_sizes = chrom_sizes
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17 self.type = bed_type
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18 if self.type == "trfbig":
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19 self.trfbig_to_gff3()
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yating-l
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20 if self.type == "regtools":
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21 self.splicejunctions_to_gff3()
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22
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yating-l
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23 def trfbig_to_gff3(self):
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24 gff3 = open(self.output, 'w')
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25 gff3.write("##gff-version 3\n")
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yating-l
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26 sizes_dict = utils.sequence_region(self.chrom_sizes)
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yating-l
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27 seq_regions = dict()
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yating-l
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28 with open(self.input, 'r') as bed:
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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29 for line in bed:
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yating-l
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30 field = OrderedDict()
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31 attribute = OrderedDict()
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yating-l
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32 li = line.rstrip().split("\t")
804a93e87cc8 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
yating-l
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33 field['seqid'] = li[0]
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34 if field['seqid'] not in seq_regions:
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35 end_region = sizes_dict[field['seqid']]
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yating-l
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36 gff3.write("##sequence-region " + field['seqid'] + ' 1 ' + str(end_region) + '\n')
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yating-l
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37 seq_regions[field['seqid']] = end_region
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38 field['source'] = li[3]
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39 field['type'] = 'tandem_repeat'
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40 # The first base in a chromosome is numbered 0 in BED format
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yating-l
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41 field['start'] = str(int(li[1]) + 1)
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42 field['end'] = li[2]
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43 field['score'] = li[9]
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44 field['strand'] = '+'
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45 field['phase'] = '.'
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46 attribute['length of repeat unit'] = li[4]
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47 attribute['mean number of copies of repeat'] = li[5]
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48 attribute['length of consensus sequence'] = li[6]
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49 attribute['percentage match'] = li[7]
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50 attribute['percentage indel'] = li[8]
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51 attribute['percent of a\'s in repeat unit'] = li[10]
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52 attribute['percent of c\'s in repeat unit'] = li[11]
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yating-l
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53 attribute['percent of g\'s in repeat unit'] = li[12]
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yating-l
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54 attribute['percent of t\'s in repeat unit'] = li[13]
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55 attribute['entropy'] = li[14]
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56 attribute['sequence of repeat unit element'] = li[15]
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yating-l
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57 utils.write_features(field, attribute, gff3)
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58 gff3.close()
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59
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60
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61 def splicejunctions_to_gff3(self):
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62 gff3 = open(self.output, 'w')
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63 gff3.write("##gff-version 3\n")
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yating-l
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64 sizes_dict = utils.sequence_region(self.chrom_sizes)
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65 seq_regions = dict()
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66 with open(self.input, 'r') as bed:
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67 for line in bed:
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68 field = OrderedDict()
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69 attribute = OrderedDict()
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70 li = line.rstrip().split("\t")
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71 field['seqid'] = li[0]
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72 if field['seqid'] not in seq_regions:
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73 end_region = sizes_dict[field['seqid']]
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74 gff3.write("##sequence-region " + field['seqid'] + ' 1 ' + str(end_region) + '\n')
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75 seq_regions[field['seqid']] = end_region
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76 field['source'] = li[3]
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77 field['type'] = 'junction'
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78 # The first base in a chromosome is numbered 0 in BED format
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79 field['start'] = int(li[1]) + 1
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80 field['end'] = li[2]
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81 field['score'] = li[12]
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82 field['strand'] = li[5]
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83 field['phase'] = '.'
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84 attribute['ID'] = li[3]
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85 attribute['Name'] = li[3]
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86 attribute['blockcount'] = li[9]
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87 attribute['blocksizes'] = li[10]
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88 attribute['chromstarts'] = li[11]
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89 utils.write_features(field, attribute, gff3)
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90 utils.child_blocks(field, attribute, gff3)
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91 gff3.close()
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92