frozenleaves/biopython
1
0
Fork 0
mirror of https://github.com/biopython/biopython.git synced 2025-10-20 13:43:47 +08:00
Code Issues Packages Projects Releases Wiki Activity

Bio.Align exonerate, avoid next() so we can use NamedTemporaryFile (#4948)

Browse Source 
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local>
This commit is contained in:
mdehoon
2025-02-24 23:01:06 +09:00
committed by GitHub
parent c3c9c736d6
commit bbf3a40ed0
1 changed files with 8 additions and 9 deletions
Download Patch File Download Diff File Expand all files Collapse all files

17
Bio/Align/exonerate.py
View File

@ -430,14 +430,14 @@ class AlignmentIterator(interfaces.AlignmentIterator):
def _read_header(self, stream):
self.metadata = {}
self.metadata["Program"] = "exonerate"
line = next(stream)
line = stream.readline()
prefix = "Command line: "
assert line.startswith(prefix)
commandline = line[len(prefix) :].strip()
assert commandline.startswith("[")
assert commandline.endswith("]")
self.metadata["Command line"] = commandline[1:-1]
line = next(stream)
line = stream.readline()
prefix = "Hostname: "
assert line.startswith(prefix)
hostname = line[len(prefix) :].strip()
@ -637,13 +637,12 @@ class AlignmentIterator(interfaces.AlignmentIterator):
for line in stream:
line = line.strip()
if line == "-- completed exonerate analysis":
try:
next(stream)
except StopIteration:
return
raise ValueError(
"Found additional data after 'completed exonerate analysis'; corrupt file?"
)
line = stream.readline()
if line:
raise ValueError(
"Found additional data after 'completed exonerate analysis'; corrupt file?"
)
return
if line.startswith("vulgar: "):
words = line[8:].split()
alignment = self._parse_vulgar(words)