Mercurial > repos > yating-l > jbrowsearchivecreator

comparison utils.py @ 15:671231da45f9 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 594c5fa1e3cdb378ecf6b5490ec2cbac5fa8a61e-dirty
author yating-l
date Wed, 05 Jul 2017 15:47:15 -0400
parents 8d1cf7ce65cd
children
comparison
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14:f4a9197281d5 15:671231da45f9
55 for line in sizes: 55 for line in sizes:
56 chrom_info = line.rstrip().split('\t') 56 chrom_info = line.rstrip().split('\t')
57 sizes_dict[chrom_info[0]] = chrom_info[1] 57 sizes_dict[chrom_info[0]] = chrom_info[1]
58 return sizes_dict 58 return sizes_dict
59 59
60 def child_blocks(parent_field, parent_attr, gff3): 60 def child_blocks(parent_field, parent_attr, gff3, child_type):
61 num = 0 61 num = 0
62 blockcount = int(parent_attr['blockcount']) 62 blockcount = int(parent_attr['blockcount'])
63 chromstart = parent_attr['chromstarts'].split(',') 63 chromstart = parent_attr['chromstarts'].split(',')
64 blocksize = parent_attr['blocksizes'].split(',') 64 blocksize = parent_attr['blocksizes'].split(',')
65 parent_start = parent_field['start']
65 while num < blockcount: 66 while num < blockcount:
66 child_attr = OrderedDict() 67 child_attr = OrderedDict()
67 child_field = parent_field 68 child_field = parent_field
68 child_field['type'] = 'exon_junction' 69 child_field['type'] = child_type
69 child_field['start'] = int(chromstart[num]) + int(parent_field['start']) 70 child_field['start'] = int(chromstart[num]) + int(parent_start)
70 child_field['end'] = int(child_field['start']) + int(blocksize[num]) - 1 71 child_field['end'] = int(child_field['start']) + int(blocksize[num]) - 1
71 child_attr['ID'] = parent_attr['ID'] + '_exon_' + str(num+1) 72 child_attr['ID'] = parent_attr['ID'] + '_part_' + str(num+1)
72 child_attr['Parent'] = parent_attr['ID'] 73 child_attr['Parent'] = parent_attr['ID']
73 write_features(child_field, child_attr, gff3) 74 write_features(child_field, child_attr, gff3)
74 num = num + 1 75 num = num + 1
75 76
76 def add_tracks_to_json(trackList_json, new_tracks, modify_type): 77 def add_tracks_to_json(trackList_json, new_tracks, modify_type):