jlec 14/05/07 11:00:43
Added: SffIO_broken_padding.patch
SffIO_error_in_check_eof.patch
Log:
sci-biology/biopython: Import changes from sci overlay
(Portage version: 2.2.10/cvs/Linux x86_64, signed Manifest commit with key
B9D4F231BD1558AB!)
Revision Changes Path
1.1 sci-biology/biopython/files/SffIO_broken_padding.patch
file :
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/biopython/files/SffIO_broken_padding.patch?rev=1.1&view=markup
plain:
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/biopython/files/SffIO_broken_padding.patch?rev=1.1&content-type=text/plain
Index: SffIO_broken_padding.patch
===================================================================
diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
index 735d55b..b89cf41 100644
--- a/Bio/SeqIO/SffIO.py
+++ b/Bio/SeqIO/SffIO.py
@@ -933,12 +933,20 @@ def _check_eof(handle, index_offset, index_length):
"null padding region ended '.sff' which could "
"be the start of a concatenated SFF file? "
"See offset %i" % (padding, offset))
+ if padding and not extra:
+ #TODO - Is this error harmless enough to just ignore?
+ import warnings
+ from Bio import BiopythonParserWarning
+ warnings.warn("Your SFF file is technically invalid as it is missing "
+ "a terminal %i byte null padding region." % padding,
+ BiopythonParserWarning)
+ return
if extra.count(_null) != padding:
import warnings
from Bio import BiopythonParserWarning
warnings.warn("Your SFF file is invalid, post index %i byte "
- "null padding region contained data." % padding,
- BiopythonParserWarning)
+ "null padding region contained data: %r"
+ % (padding, extra), BiopythonParserWarning)
offset = handle.tell()
assert offset % 8 == 0, \
1.1 sci-biology/biopython/files/SffIO_error_in_check_eof.patch
file :
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/biopython/files/SffIO_error_in_check_eof.patch?rev=1.1&view=markup
plain:
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/biopython/files/SffIO_error_in_check_eof.patch?rev=1.1&content-type=text/plain
Index: SffIO_error_in_check_eof.patch
===================================================================
diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
index 2bb0dac..735d55b 100644
--- a/Bio/SeqIO/SffIO.py
+++ b/Bio/SeqIO/SffIO.py
@@ -941,7 +941,8 @@ def _check_eof(handle, index_offset, index_length):
BiopythonParserWarning)
offset = handle.tell()
- assert offset % 8 == 0
+ assert offset % 8 == 0, \
+ "Wanted offset %i %% 8 = %i to be zero" % (offset, offset % 8)
# Should now be at the end of the file...
extra = handle.read(4)
if extra == _sff:
