运行命令${src}/cuffmerge -o ./merge -g ${input}/gencode.v44.primary_assembly.annotation_sorted.gtf merge.list时报错：
run_log = open(logging_dir + "run.log", "w", 0)
ValueError: can't have unbuffered text I/O
解决方案：修改${src}/cuffmerge代码。
修改第一处：在${src}/cuffmerge的第53行插入以下代码
class Unbuffered(object):
def __init__(self, stream):
self.stream = stream
def write(self, data):
self.stream.write(data)
self.stream.flush()
def writelines(self, datas):
self.stream.writelines(datas)
self.stream.flush()
def __getattr__(self, attr):
return getattr(self.stream, attr)
效果如下所示：
修改第二处：
把在${src}/cuffmerge的第526行代码run_log = open(logging_dir + "run.log", "w", 0)改为run_log = Unbuffered(open(logging_dir + "run.log", "w"))
效果如下所示：
代码来源：https://github.com/cole-trapnell-lab/cufflinks/issues/130
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