Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/FastaParser.py @ 18:94ab73e8a190
Uploaded
author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
parents | 769e306b7933 |
children | 0ab839023fe4 |
comparison
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17:b0e8584489e6 | 18:94ab73e8a190 |
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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] | 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 |