Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/FastaParser.py @ 31:0ab839023fe4
Uploaded
author | m-zytnicki |
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date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 94ab73e8a190 |
children |
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30:5677346472b5 | 31:0ab839023fe4 |
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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].replace("|", "_").replace(".", "_") | 83 name = self.currentLine[1:].split()[0] |
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].replace("|", "_").replace(".", "_") | 92 name = line[1:].split()[0] |
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 |