本文整理汇总了Python中Bio.Align.Generic.Alignment._star_info方法的典型用法代码示例。如果您正苦于以下问题：Python Alignment._star_info方法的具体用法？Python Alignment._star_info怎么用？Python Alignment._star_info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Bio.Align.Generic.Alignment的用法示例。
在下文中一共展示了Alignment._star_info方法的1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: next
# 需要导入模块: from Bio.Align.Generic import Alignment [as 别名]
# 或者: from Bio.Align.Generic.Alignment import _star_info [as 别名]
#.........这里部分代码省略.........
if not line : break #end of file
assert line.strip() == ""
assert seq_cols is not None
#Confirm all same length
for s in seqs:
assert len(s) == len(seqs[0])
if consensus:
assert len(consensus) == len(seqs[0])
#Loop over any remaining blocks...
done = False
while not done:
#There should be a blank line between each block.
#Also want to ignore any consensus line from the
#previous block.
while (not line) or line.strip() == "":
line = handle.readline()
if not line : break # end of file
if not line : break # end of file
if line.split(None,1)[0] in known_headers:
#Found concatenated alignment.
done = True
self._header = line
break
for i in range(len(ids)):
assert line[0] != " ", "Unexpected line:\n%s" % repr(line)
fields = line.rstrip().split()
#We expect there to be two fields, there can be an optional
#"sequence number" field containing the letter count.
if len(fields) < 2 or len(fields) > 3:
raise ValueError("Could not parse line:\n%s" % repr(line))
if fields[0] != ids[i]:
raise ValueError("Identifiers out of order? Got '%s' but expected '%s'" \
% (fields[0], ids[i]))
if fields[1] != line[seq_cols]:
start = len(fields[0]) + line[len(fields[0]):].find(fields[1])
assert start == seq_cols.start, 'Old location %s -> %i:XX' % (seq_cols, start)
end = start + len(fields[1])
seq_cols = slice(start, end)
del start, end
#Append the sequence
seqs[i] += fields[1]
assert len(seqs[i]) == len(seqs[0])
if len(fields) == 3:
#This MAY be an old style file with a letter count...
try:
letters = int(fields[2])
except ValueError:
raise ValueError("Could not parse line, bad sequence number:\n%s" % line)
if len(seqs[i].replace("-","")) != letters:
raise ValueError("Could not parse line, invalid sequence number:\n%s" % line)
#Read in the next line
line = handle.readline()
#There should now be a consensus line
if consensus:
assert line[0] == " "
assert seq_cols is not None
consensus += line[seq_cols]
assert len(consensus) == len(seqs[0])
assert not line[:seq_cols.start].strip()
assert not line[seq_cols.stop:].strip()
#Read in the next line
line = handle.readline()
assert len(ids) == len(seqs)
if len(seqs) == 0 or len(seqs[0]) == 0:
return None
if self.records_per_alignment is not None \
and self.records_per_alignment != len(ids):
raise ValueError("Found %i records in this alignment, told to expect %i" \
% (len(ids), self.records_per_alignment))
alignment = Alignment(self.alphabet)
alignment_length = len(seqs[0])
for i in range(len(ids)):
if len(seqs[i]) != alignment_length:
raise ValueError("Error parsing alignment - sequences of different length?")
alignment.add_sequence(ids[i], seqs[i])
#TODO - Handle alignment annotation better, for now
#mimic the old parser in Bio.Clustalw
if version:
alignment._version = version
if consensus:
assert len(consensus) == alignment_length, \
"Alignment length is %i, consensus length is %i, '%s'" \
% (alignment_length, len(consensus), consensus)
alignment._star_info = consensus
return alignment