Mercurial > repos > yufei-luo > s_mart

comparison commons/core/parsing/FindRep.py @ 36:44d5973c188c

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
parents 769e306b7933
children
comparison
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35:d94018ca4ada 36:44d5973c188c
1 import re
2 from xml.sax.handler import ContentHandler
3
4 class FindRep( ContentHandler ):
5 def __init__(self,outfileName, filter=0,count=0):
6 self.inWindowContent = 0
7 self.inSeqNameContent = 0
8 self.inStartContent = 0
9 self.inEndContent = 0
10 self.inPeriodContent = 0
11 self.inUnitContent = 0
12 self.inScoreContent = 0
13 self.count = count
14 self._outfileName = outfileName
15 self.filter=filter
16
17 def startDocument(self):
18 self._fileout = open(self._outfileName,"w")
19
20 def startElement(self,name,attrs):
21 if name=="window":
22 self.inWindowContent=1
23 elif name=="sequence-name":
24 self.inSeqNameContent=1
25 self.seqname=""
26 elif name=="repeat":
27 self.inRepContent=1
28 self.start=""
29 self.end=""
30 self.period=""
31 self.type={}
32 elif name=="start":
33 self.inStartContent=1
34 elif name=="end":
35 self.inEndContent=1
36 elif name=="period":
37 self.inPeriodContent=1
38 elif name=="unit":
39 self.inUnitContent=1
40 self.unit=""
41 elif name=="score":
42 self.inScoreContent=1
43 self.score=""
44
45 def characters(self,ch):
46 if self.inSeqNameContent:
47 self.seqname+=ch
48 elif self.inStartContent:
49 self.start+=ch
50 elif self.inEndContent:
51 self.end+=ch
52 elif self.inPeriodContent:
53 self.period+=ch
54 elif self.inUnitContent:
55 self.unit+=ch
56 elif self.inScoreContent:
57 self.score+=ch
58
59 def endElement(self,name):
60 if name=="window":
61 self.inWindowContent=0
62 elif name=="sequence-name":
63 self.inSeqNameContent=0
64 elif name=="repeat":
65 self.inRepContent=0
66 start=int(self.start)
67 end=int(self.end)
68 period=int(self.period)
69 score=float(self.score)
70 if score>self.filter:
71 return
72 max = 0
73 self.count+=1
74 for k,n in self.type.items():
75 if n>max:
76 max = n
77 k_max = k
78
79 m=re.match("^[0-9]+.+\{Cut\}",self.seqname)
80 if m!=None:
81 seqname=self.seqname[m.start(0):m.end(0)-5].rstrip()
82 seqname=re.sub("^[0-9]+ ","",seqname).lstrip()
83 tok=self.seqname[m.end(0):].split("..")
84 astart=start+int(tok[0])-1
85 aend=end+int(tok[0])-1
86 else:
87 astart=start
88 aend=end
89 seqname=self.seqname
90 if len(k_max) > 100:
91 k_max=k_max[:48]+"..."+k_max[-51:]
92 strout="%d\t(%s)%d\t%s\t%d\t%d"%\
93 (self.count,k_max,(abs(start-end)+1)/period,\
94 seqname,astart,aend)
95 self._fileout.write("%s\n"%(strout))
96
97 elif name=="start":
98 self.inStartContent=0
99 elif name=="end":
100 self.inEndContent=0
101 elif name=="period":
102 self.inPeriodContent=0
103 elif name=="score":
104 self.inScoreContent=0
105 elif name=="unit":
106 self.inUnitContent=0
107 if self.type.has_key(self.unit):
108 self.type[self.unit]+=1
109 else:
110 self.type[self.unit]=1
111
112 def endDocument(self):
113 self._fileout.close()