本文整理汇总了Python中galaxy.datatypes.data.Text.merge方法的典型用法代码示例。如果您正苦于以下问题：Python Text.merge方法的具体用法？Python Text.merge怎么用？Python Text.merge使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类galaxy.datatypes.data.Text的用法示例。
在下文中一共展示了Text.merge方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: merge
# 需要导入模块: from galaxy.datatypes.data import Text [as 别名]
# 或者: from galaxy.datatypes.data.Text import merge [as 别名]
def merge(split_files, output_file):
"""Merging multiple MIRA files is non-trivial and may not be possible..."""
if len(split_files) == 1:
#For one file only, use base class method (move/copy)
return Text.merge(split_files, output_file)
if not split_files:
raise ValueError("Given no MIRA, %r, to merge into %s" \
% (split_files, output_file))
raise NotImplementedError("Merging MIRA Assembly Files has not been implemented")示例2: merge
# 需要导入模块: from galaxy.datatypes.data import Text [as 别名]
# 或者: from galaxy.datatypes.data.Text import merge [as 别名]
def merge(split_files, output_file):
"""Merging multiple XML files is non-trivial and must be done in subclasses."""
if len(split_files) == 1:
#For one file only, use base class method (move/copy)
return Text.merge(split_files, output_file)
if not split_files:
raise ValueError("Given no BLAST XML files, %r, to merge into %s" \
% (split_files, output_file))
out = open(output_file, "w")
h = None
for f in split_files:
if not os.path.isfile(f):
log.warning("BLAST XML file %s missing, retry in 1s..." % f)
sleep(1)
if not os.path.isfile(f):
log.error("BLAST XML file %s missing" % f)
raise ValueError("BLAST XML file %s missing" % f)
h = open(f)
body = False
header = h.readline()
if not header:
out.close()
h.close()
#Retry, could be transient error with networked file system...
log.warning("BLAST XML file %s empty, retry in 1s..." % f)
sleep(1)
h = open(f)
header = h.readline()
if not header:
log.error("BLAST XML file %s was empty" % f)
raise ValueError("BLAST XML file %s was empty" % f)
if header.strip() != '<?xml version="1.0"?>':
out.write(header) #for diagnosis
out.close()
h.close()
raise ValueError("%s is not an XML file!" % f)
line = h.readline()
header += line
if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">',
'<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']:
out.write(header) #for diagnosis
out.close()
h.close()
raise ValueError("%s is not a BLAST XML file!" % f)
while True:
line = h.readline()
if not line:
out.write(header) #for diagnosis
out.close()
h.close()
raise ValueError("BLAST XML file %s ended prematurely" % f)
header += line
if "<Iteration>" in line:
break
if len(header) > 10000:
#Something has gone wrong, don't load too much into memory!
#Write what we have to the merged file for diagnostics
out.write(header)
out.close()
h.close()
raise ValueError("BLAST XML file %s has too long a header!" % f)
if "<BlastOutput>" not in header:
out.close()
h.close()
raise ValueError("%s is not a BLAST XML file:\n%s\n..." % (f, header))
if f == split_files[0]:
out.write(header)
old_header = header
elif old_header[:300] != header[:300]:
#Enough to check <BlastOutput_program> and <BlastOutput_version> match
out.close()
h.close()
raise ValueError("BLAST XML headers don't match for %s and %s - have:\n%s\n...\n\nAnd:\n%s\n...\n" \
% (split_files[0], f, old_header[:300], header[:300]))
else:
out.write(" <Iteration>\n")
for line in h:
if "</BlastOutput_iterations>" in line:
break
#TODO - Increment <Iteration_iter-num> and if required automatic query names
#like <Iteration_query-ID>Query_3</Iteration_query-ID> to be increasing?
out.write(line)
h.close()
out.write(" </BlastOutput_iterations>\n")
out.write("</BlastOutput>\n")
out.close()