Mercurial > repos > jankanis > blast2html

comparison blast2html.py @ 69:0c4ac210068b

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author Jan Kanis <jan.code@jankanis.nl>
date Wed, 18 Jun 2014 14:12:00 +0200
parents fa8a93bdefd7
children 371cd585e459
comparison
equal deleted inserted replaced
68:fa8a93bdefd7 69:0c4ac210068b
85 def alignment_pre(hsp): 85 def alignment_pre(hsp):
86 """Create the preformatted alignment blocks""" 86 """Create the preformatted alignment blocks"""
87 87
88 step = 60 88 step = 60
89 89
90 def split(txt):
91 return [txt[i:i+step] for i in range(0, len(txt), step)]
92
93 qfrom = int(hsp['Hsp_query-from']) 90 qfrom = int(hsp['Hsp_query-from'])
94 qto = int(hsp['Hsp_query-to']) 91 qto = int(hsp['Hsp_query-to'])
92 qframe = int(hsp['Hsp_query-frame'])
95 hfrom = int(hsp['Hsp_hit-from']) 93 hfrom = int(hsp['Hsp_hit-from'])
96 hto = int(hsp['Hsp_hit-to']) 94 hto = int(hsp['Hsp_hit-to'])
95 hframe = int(hsp['Hsp_hit-frame'])
97 qseq = hsp.Hsp_qseq.text 96 qseq = hsp.Hsp_qseq.text
98 midline = hsp.Hsp_midline.text 97 midline = hsp.Hsp_midline.text
99 hseq = hsp.Hsp_hseq.text 98 hseq = hsp.Hsp_hseq.text
100 99
101 offset = 0 100 if not qframe in [1, -1]:
101 warnings.warn("Error in BlastXML input: Hsp node {} has a Hsp_query-frame of {}".format(nodeid(hsp), qframe))
102 qframe = -1 if qframe < 0 else 1
103 if not hframe in [1, -1]:
104 warnings.warn("Error in BlastXML input: Hsp node {} has a Hsp_hit-frame of {}".format(nodeid(hsp), hframe))
105 hframe = -1 if hframe < 0 else 1
106
107 def split(txt):
108 return [txt[i:i+step] for i in range(0, len(txt), step)]
109
102 for qs, mid, hs, offset in zip(split(qseq), split(midline), split(hseq), range(0, len(qseq), step)): 110 for qs, mid, hs, offset in zip(split(qseq), split(midline), split(hseq), range(0, len(qseq), step)):
103 yield ( 111 yield (
104 "Query {:>7} {} {}\n".format(qfrom+offset, qs, qfrom+offset+len(qs)-1) + 112 "Query {:>7} {} {}\n".format(qfrom+offset*qframe, qs, qfrom+(offset+len(qs)-1)*qframe) +
105 " {:7} {}\n".format('', mid) + 113 " {:7} {}\n".format('', mid) +
106 "Subject{:>7} {} {}".format(hfrom+offset, hs, hfrom+offset+len(hs)-1) 114 "Subject{:>7} {} {}".format(hfrom+offset*hframe, hs, hfrom+(offset+len(hs)-1)*hframe)
107 ) 115 )
108 116
109 if qfrom+len(qseq)-1 != qto: 117 if qfrom+(len(qseq)-1)*qframe != qto:
110 warnings.warn("Error in BlastXML input: Hsp node {} qseq length mismatch: from {} to {} length {}".format( 118 warnings.warn("Error in BlastXML input: Hsp node {} qseq length mismatch: from {} to {} length {}".format(
111 nodeid(hsp), qfrom, qto, len(qseq))) 119 nodeid(hsp), qfrom, qto, len(qseq)))
112 if hfrom+len(hseq)-1 != hto: 120 if hfrom+(len(hseq)-1)*hframe != hto:
113 warnings.warn("Error in BlastXML input: Hsp node {} hseq length mismatch: from {} to {} length {}".format( 121 warnings.warn("Error in BlastXML input: Hsp node {} hseq length mismatch: from {} to {} length {}".format(
114 nodeid(hsp), hfrom, hto, len(hseq))) 122 nodeid(hsp), hfrom, hto, len(hseq)))
115 123
116 124
117 125