Mercurial > repos > yufei-luo > s_mart

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

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Uploaded
author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents 769e306b7933
children
comparison
equal deleted inserted replaced
17:b0e8584489e6 18:94ab73e8a190
121 m1 = re.search(r"^\s*-?\d+\.?\d*\s*$", line) 121 m1 = re.search(r"^\s*-?\d+\.?\d*\s*$", line)
122 m2 = re.search(r"^\s*(\d+)\s+-?\d+\.?\d*\s*$", line) 122 m2 = re.search(r"^\s*(\d+)\s+-?\d+\.?\d*\s*$", line)
123 m3 = re.search(r"^\s*fixedStep\s+chrom=(\S+)\s+start=(\d+)\s+step=1\s*$", line) 123 m3 = re.search(r"^\s*fixedStep\s+chrom=(\S+)\s+start=(\d+)\s+step=1\s*$", line)
124 m4 = re.search(r"^\s*fixedStep\s+chrom=\S+\s+start=\d+\s+step=\d+\s+span=\d+\s*$", line) 124 m4 = re.search(r"^\s*fixedStep\s+chrom=\S+\s+start=\d+\s+step=\d+\s+span=\d+\s*$", line)
125 m5 = re.search(r"^\s*variableStep\s+chrom=(\S+)\s*$", line) 125 m5 = re.search(r"^\s*variableStep\s+chrom=(\S+)\s*$", line)
126 m6 = re.search(r"^\s*variableStep\s+chrom=(\S+)span=(\d+)\s*$", line) 126 m6 = re.search(r"^\s*variableStep\s+chrom=(\S+)\s+span=(\d+)\s*$", line)
127 127
128 if m1 != None: 128 if m1 != None:
129 outputFile.write(struct.pack("Q", mark)) 129 outputFile.write(struct.pack("Q", mark))
130 index += 1 130 index += 1
131 elif m2 != None: 131 elif m2 != None:
154 outputFile = open(self.makeIndexName(newChromosome), "wb") 154 outputFile = open(self.makeIndexName(newChromosome), "wb")
155 index = 0 155 index = 0
156 outputFile.write(self.filler) 156 outputFile.write(self.filler)
157 chromosome = newChromosome 157 chromosome = newChromosome
158 elif m6 != None: 158 elif m6 != None:
159 raise Exception("Error! Cannot parse variable step WIG files with step > 1 or span > 1") 159 if m6.group(2) != "1":
160 raise Exception("Error! Cannot parse variable step WIG files with step > 1 or span > 1")
161 newChromosome = m6.group(1)
162 if newChromosome != chromosome:
163 if outputFile != None:
164 outputFile.close()
165 outputFile = open(self.makeIndexName(newChromosome), "wb")
166 index = 0
167 outputFile.write(self.filler)
168 chromosome = newChromosome
160 elif (len(line) == 0) or line[0] == "#" or line.startswith("track"): 169 elif (len(line) == 0) or line[0] == "#" or line.startswith("track"):
161 pass 170 pass
162 else: 171 else:
163 raise Exception("Error! Cannot understand line '%s' of WIG file while creating index file! Aborting." % (line)) 172 raise Exception("Error! Cannot understand line '%s' of WIG file while creating index file! Aborting." % (line))
164 173