1 # $Id: BUGS,v 1.6 2004-02-24 19:58:26 bosborne Exp $
8 * The StandAloneBlast.t test is failing on cygwin installations (and
9 nowhere else). We suspect something to do with temporary file
10 opening. Fixed in 1.4 (set TMPDIR).
15 * Bio::Tools::Blast continues to cause problems for some people. As
16 it is not actively maintained there are a slew of reported bugs for
17 it that have not been fixed.
19 * Bio::Tools::Run::Alignment::TCoffee - t_coffee binary does not get
20 all parameters it needs when aligning (two) two DNA sequences
23 * Bio::Tools::Run::ClustalW and t/ClustalW will report errors for
24 clustalw versions 1.8x due to a bug in clustalw.
26 * Bio::DB::GenBank continues to have intermittent errors. Bio::DB::GDB
27 is also unreliable at times and one can safely ignore errors from
28 these during a make test.
29 Bio::DB::GenBank is unable to download whole contig files as well
30 as NCBI ref seqs like NT_* numbers unless the -format flag is
31 passed in and specified as 'fasta' in the constructor.
32 get_Stream_by_batch() also has intermittent errors which are being
38 * NCBI has changed some of the cgi scripts for retrieving sequences
39 online which as resulted in some of the DB methods from not working
40 consistently. We are addressing these in the 0.9.x and 1.0 series
41 of releases. We recommend using the Bio::DB::EMBL object that is
42 part of the later releases.
44 Additionally RefSeq Contigs are not properly downloaded, please see
45 the bioperl list archives for information about potential
46 workarounds and ongoing development effort to address these.
50 * Bio::Tools::BPlite does not parse and set frame properly for
51 tblastx reports (Jitterbug bug # 978).
53 * Bio::Tools::BPlite interface needs to be updated to fix parsing
54 more than bl2seq report report (Jitterbug bug #940), this has been
55 fixed on the main code trunk and will be part of the next major
58 * If File::Temp is not installed, tempdirs are not cleaned up
59 properly. This is fixed on main code trunk with the introduction
60 of rmtree method in Bio::Root::IO, however, it is best to install
61 File::Temp when running 0.7 branch code.
63 * Bio::Tools::Blast does not allow users to run blast, instead use
64 Bio::Tools::Run::StandAloneBlast to run local blasts. To submit
65 jobs to a remote blast server like NCBI a module
66 Bio::Tools::Run::RemoteBlast has been written but is part of the
67 main trunk code and must be obtained through CVS until the next
68 major bioperl release.
72 * Bio::Tools::BPlite doc error lists
74 my $parser = new BPlite(\*FH);
76 my $parser = new Bio::Tools::BPlite(\*FH);