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comparison blast2html.py @ 68:fa8a93bdefd7

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fix bug in calculations of alignment end
author Jan Kanis <jan.code@jankanis.nl>
date Wed, 18 Jun 2014 12:25:37 +0200
parents 19c48f2ec775
children 0c4ac210068b
comparison
equal deleted inserted replaced
67:19c48f2ec775 68:fa8a93bdefd7
81 return hitid 81 return hitid
82 82
83 83
84 @filter 84 @filter
85 def alignment_pre(hsp): 85 def alignment_pre(hsp):
86 """Create the preformatted alignment blocks"""
87
86 step = 60 88 step = 60
87 89
88 def split(txt): 90 def split(txt):
89 return [txt[i:i+step] for i in range(0, len(txt), step)] 91 return [txt[i:i+step] for i in range(0, len(txt), step)]
90 92
97 hseq = hsp.Hsp_hseq.text 99 hseq = hsp.Hsp_hseq.text
98 100
99 offset = 0 101 offset = 0
100 for qs, mid, hs, offset in zip(split(qseq), split(midline), split(hseq), range(0, len(qseq), step)): 102 for qs, mid, hs, offset in zip(split(qseq), split(midline), split(hseq), range(0, len(qseq), step)):
101 yield ( 103 yield (
102 "Query {:>7} {} {}\n".format(qfrom+offset, qs, qfrom+len(qs)-1) + 104 "Query {:>7} {} {}\n".format(qfrom+offset, qs, qfrom+offset+len(qs)-1) +
103 " {:7} {}\n".format('', mid) + 105 " {:7} {}\n".format('', mid) +
104 "Subject{:>7} {} {}".format(hfrom+offset, hs, hfrom+len(hs)-1) 106 "Subject{:>7} {} {}".format(hfrom+offset, hs, hfrom+offset+len(hs)-1)
105 ) 107 )
106 108
107 if qfrom+len(qseq)-1 != qto: 109 if qfrom+len(qseq)-1 != qto:
108 warnings.warn("Error in BlastXML input: Hsp node {} qseq length mismatch: from {} to {} length {}".format( 110 warnings.warn("Error in BlastXML input: Hsp node {} qseq length mismatch: from {} to {} length {}".format(
109 nodeid(hsp), qfrom, qto, len(qseq))) 111 nodeid(hsp), qfrom, qto, len(qseq)))