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Remove outer try/except in Eland sniffer

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Exceptions in a sniffer are already caught in
galaxy.datatypes.sniff.guess_ext() and are equivalent to `return False`.
Thanks @nsoranzo!
This commit is contained in:
mvdbeek
2017-07-03 13:25:35 +02:00
parent cbcee585b5
commit e379f44eff
1 changed files with 28 additions and 31 deletions
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lib/galaxy/datatypes/tabular.py
+28 -31
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@@ -787,37 +787,34 @@ class Eland( Tabular ):
- LANE, TILEm X, Y, INDEX, READ_NO, SEQ, QUAL, POSITION, *STRAND, FILT must be correct
- We will only check that up to the first 5 alignments are correctly formatted.
"""
try:
with compression_utils.get_fileobj(filename, gzip_only=True) as fh:
count = 0
while True:
line = fh.readline()
line = line.strip()
if not line:
break # EOF
if line:
line_pieces = line.split('\t')
if len(line_pieces) != 22:
return False
try:
if long(line_pieces[1]) < 0:
raise Exception('Out of range')
if long(line_pieces[2]) < 0:
raise Exception('Out of range')
if long(line_pieces[3]) < 0:
raise Exception('Out of range')
int(line_pieces[4])
int(line_pieces[5])
# can get a lot more specific
except ValueError:
return False
count += 1
if count == 5:
break
if count > 0:
return True
except Exception:
pass
with compression_utils.get_fileobj(filename, gzip_only=True) as fh:
count = 0
while True:
line = fh.readline()
line = line.strip()
if not line:
break # EOF
if line:
line_pieces = line.split('\t')
if len(line_pieces) != 22:
return False
try:
if long(line_pieces[1]) < 0:
raise Exception('Out of range')
if long(line_pieces[2]) < 0:
raise Exception('Out of range')
if long(line_pieces[3]) < 0:
raise Exception('Out of range')
int(line_pieces[4])
int(line_pieces[5])
# can get a lot more specific
except ValueError:
return False
count += 1
if count == 5:
break
if count > 0:
return True
return False
def set_meta( self, dataset, overwrite=True, skip=None, max_data_lines=5, **kwd ):