Mercurial > repos > yufei-luo > s_mart

comparison commons/core/parsing/FastaParser.py @ 18:94ab73e8a190

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Uploaded
author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents 769e306b7933
children 0ab839023fe4
comparison
equal deleted inserted replaced
17:b0e8584489e6 18:94ab73e8a190
78 string = "" 78 string = ""
79 79
80 if self.currentLine != None: 80 if self.currentLine != None:
81 if self.currentLine[0] != ">": 81 if self.currentLine[0] != ">":
82 raise Exception("First line is weird: %s" % (self.currentLine)) 82 raise Exception("First line is weird: %s" % (self.currentLine))
83 name = self.currentLine[1:].split()[0] 83 name = self.currentLine[1:].split()[0].replace("|", "_").replace(".", "_")
84 self.currentLine = None 84 self.currentLine = None
85 85
86 for line in self.handle: 86 for line in self.handle:
87 line = line.strip() 87 line = line.strip()
88 if line == "": 88 if line == "":
89 pass 89 pass
90 elif line[0] == ">": 90 elif line[0] == ">":
91 if name == None: 91 if name == None:
92 name = line[1:].split()[0] 92 name = line[1:].split()[0].replace("|", "_").replace(".", "_")
93 else: 93 else:
94 self.currentLine = line 94 self.currentLine = line
95 return Sequence(name, string) 95 return Sequence(name, string)
96 else: 96 else:
97 string += line 97 string += line