Mercurial > repos > jankanis > blast2html

comparison blast_html.py @ 14:0b33898bba45

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small bugfixes (one for python 3.4)
author Jan Kanis <jan.code@jankanis.nl>
date Mon, 12 May 2014 17:32:01 +0200
parents c2d63adb83db
children 648b3b7437da
comparison
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13:c2d63adb83db 14:0b33898bba45
69 return hit.Hit_id.text.split('|', 2)[2] 69 return hit.Hit_id.text.split('|', 2)[2]
70 70
71 @filter 71 @filter
72 def alignment_pre(hsp): 72 def alignment_pre(hsp):
73 return ( 73 return (
74 "Query {:>7s} {} {}\n".format(hsp['Hsp_query-from'], hsp.Hsp_qseq, hsp['Hsp_query-to']) + 74 "Query {:>7s} {} {}\n".format(hsp['Hsp_query-from'].text, hsp.Hsp_qseq, hsp['Hsp_query-to'].text) +
75 " {:7s} {}\n".format('', hsp.Hsp_midline) + 75 " {:7s} {}\n".format('', hsp.Hsp_midline) +
76 "Subject{:>7s} {} {}".format(hsp['Hsp_hit-from'], hsp.Hsp_hseq, hsp['Hsp_hit-to']) 76 "Subject{:>7s} {} {}".format(hsp['Hsp_hit-from'].text, hsp.Hsp_hseq, hsp['Hsp_hit-to'].text)
77 ) 77 )
78 78
79 @filter('len') 79 @filter('len')
80 def hsplen(node): 80 def hsplen(node):
81 return int(node['Hsp_align-len']) 81 return int(node['Hsp_align-len'])
103 103
104 colors = ('black', 'blue', 'green', 'magenta', 'red') 104 colors = ('black', 'blue', 'green', 'magenta', 'red')
105 105
106 max_scale_labels = 10 106 max_scale_labels = 10
107 107
108 templatename = 'visualise.html.jinja' 108 templatename = 'blast_html.html.jinja'
109 109
110 def __init__(self, input): 110 def __init__(self, input):
111 self.input = input 111 self.input = input
112 112
113 self.blast = objectify.parse(self.input).getroot() 113 self.blast = objectify.parse(self.input).getroot()