Package: python-biopython / 1.77+dfsg-2

Metadata

Package Version Patches format
python-biopython 1.77+dfsg-2 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
remove_mathml qname.patch | (download)

Bio/Entrez/DTDs/modules.ent | 7 0 + 7 - 0 !
1 file changed, 7 deletions(-)

 remove non dfsg free dtd


privacy_breach.patch | (download)

Tests/Blast/html_msgid_29_blastx_001.html | 5 2 + 3 - 0 !
1 file changed, 2 insertions(+), 3 deletions(-)

 do not use privacy-breach-logo


blastdbv4 impl.patch | (download)

Bio/Blast/Applications.py | 8 8 + 0 - 0 !
1 file changed, 8 insertions(+)

 implement blast database version 4 switch
 This patch adds support for the -blastdb_version switch of the makeblastdb
 wrapper of the library.  This originates from a workaround to fix a build test
 failure on 32 bit architecture, but the option might be interesting upstream
 as well, hence a separation of the implementation and test.
blastdbv4 test.patch | (download)

Tests/test_NCBI_BLAST_tools.py | 8 6 + 2 - 0 !
1 file changed, 6 insertions(+), 2 deletions(-)

 adapt makeblastdb wrapper test for 32 bits architecture
 This patch works around issues with testing the wrapper to makeblastdb, which
 fails to execute on 32 bit CPU architectures due to starvation of the virtual
 memory address space.  This issue is apparently specific to the construction
 of BLAST databases in version 5 format, and does not occur when falling back
 to version 4.  This requires the wrapper to know about falling back to version
 4, which is addressed by another patch.