Mercurial > repos > mahtabm > ensembl
diff variant_effect_predictor/Bio/Tools/Blast/CHANGES @ 0:1f6dce3d34e0
Uploaded
| author | mahtabm |
|---|---|
| date | Thu, 11 Apr 2013 02:01:53 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/variant_effect_predictor/Bio/Tools/Blast/CHANGES Thu Apr 11 02:01:53 2013 -0400 @@ -0,0 +1,368 @@ +Revision history for Perl extension Bio::Tools::Blast.pm and related modules. + +0.091 Thu May 18 15:15:35 2000 + (These fixes were made on both branch-06 and the main trunk). + - Fixed Webblast.pm (jitterbug PR #220). It now uses SeqIO and IO::Scalar + for sending formatted query sequence data to the BLAST servers. + - Fixed the examples/blast/ scripts related to remote BLASTing. + - Added single quotes to an '_expect' data member in Sbjct + (reported by Janet Young in jitterbug PR #218). + - Fixed regexp bug in Blast::HTML.pm that caused accessions with + . and _ characters to not be recognized. + + +0.09 Wed Mar 22 00:44:01 2000 + - Handles Blast reports that don't contain description sections. + - Handles parsing of NCBI 2.0.9 Blast2 reports. + - Identifiers of hits are assumed to be the first + chunk of non-whitespace characters in the description line + Does not assume any semantics in the structure of the identifier. + (Blast::Sbjct::_set_id() formerly attempted to extract database + name from the seq identifiers, but this was prone to breaking). + - Fixed bug in the parsing of reports that lack an hits + (incorporated code fix submitted by Michael B. Thornton + jitterbug PR#114, PR#173). + - New helper script retrieve_blast.pl added to examples/blast/ + for retrieving Blast reports from NCBI after running + run_blast_remote.pl See docs in retrieve_blast.pl for details. + - Updated Webblast.pm with new URLs for the NCBI servers. + - Fixed bug (jitterbug PR#84) in the parsing of alignments that would + cause occaisionally cause some significant hits to be missed + (incorporates code suggested by Peter van Heusden). + - Added support to Blast.pm for not parsing alignment data + using the new NO_ALIGNS parsing option. Also added -noaligns + command-line option to blast_config.pl (addresses jitterbug PR#93). + - Blast::hit() method doesn't blow up if there are no hits + (fixes jitterbug PR#129). + - Addressed jitterbug PR#96 by correcting docs. If the significance + is defined but of bad format, no default is set. + - HSP.pm properly handles bit scores expressed using floating point + and scientific notation (fixes jitterbug report PR#110). + - Fixed logic error in HSP.pm that would incorrectly throw an + exception when the number of identical residues was zero + (fixes jitterbug PR#164). + - HSP::strand() returns -1, 0, 1 instead of 'Minus', 'Plus', '' + to be in-line with with behavior of SeqFeature. + +Fixes within Bio::Root +---------------------- + - Fixed bug reported in PR#85. Bio::Root::Utilities::get_newline() + returns "\n" by default. + - IOManager::read doesn't call alarm() if it isn't available + (fixes bug #PR98). + - Root::Object::_set_io() does not pass @_ to the IOManager constructor + call (incorporates suggestion from Scot Harker, jitterbut PR#192). + + +0.085 Tue Jun 29 05:15:40 1999 (bioperl 0.05.1) +(Note: the $VERSION variable was not changed to 0.085 in this release!) + - Fixed bugs reported in PR#s: 30, 31, 41, 44, 45, 47, 48 + - Blast.pm no longer throws exceptions for hitless reports, + even if a -signif criterion is specified. + - Better support for PSI Blasts (running and parsing) based on + comments/suggestions from Ross Crowhurst and Lu Sun. + - Bug fixes in Webblast.pm regarding blastServerURL and filenames + with special characters (bug reports from James Diggans and + Bradford Powell, respectively). + - Removed =head3 tags that were causing pod2man warnings. + - Fixed -best parsing switch. + - Added better POD to Webblast.pm + +0.080 Sat Apr 24 19:39:37 1999 (bioperl 0.05) + - Complete re-implementation of the Blast report parsing strategy. + The parser now always streamifies all Blast report(s) and + segments them hit-wise instead of report-wise. This improves + performance and memory usage (but doesn't solve the memory leak). + - Documented a workaround for the memory leak (see the docs for + Blast.pm under the section "Memory Usage Issues"). + - Webblast.pm now uses LWP instead of postclient.pl to post network + Blast requests (thanks to Ross Crowhurst for code submission). + This is a much more robust mechanism, although it now requires you + to have LWP installed ("a good thing"). For example, it makes it + easy to send requests and receive results through a firewall. + It can run Blast1, Blast2, and PSI-Blast at NCBI and also supports + WashU-Blast servers. + - Fixed some miscellaneous parsing bugs and errors reported by + Greg Colello, Xie Tao, and Richard Copley from the pre-release + - Updated example/blast scripts. Renamed parse.pl and parse2.pl to + parse_blast.pl and parse_blast2.pl. parse_stream.pl is gone + (since parse_blast.pl now handles both files and streams). + Renamed run.pl to run_blast_remote.pl and added additional + options to keep it in synch with the new Webblast.pm. + + +0.075 Wed Feb 17 01:29:57 1999 (bioperl 0.04.4) + - Bug fix in Blast::Run::postclient.pl which was always printing + usage information (reported by Ross Crowhurst). + - Improved error detection & reporting in Blast::Run::Webblast + and Blast::Run::postclient.pl. + - Bug fixes in HSP.pm: _set_match_stats() now properly handles + BLASTN output format and matches() properly handles BLASTX + reports. + - Fixed detection of substitution matrix type in Blast.pm. + - Updated Blast example scripts in examples/blast/ + (in particular, run.pl). + +0.074 Wed Feb 3 04:10:06 1999 (bioperl 0.04.3) + - Modified blast_config.pl to make the -prog and -db command-line + arguments mandatory. There are no default values for $opt_blast + and $opt_db. Also removed the -dna command-line argument. + - Fixed alignment section parsing bug in Blast.pm (bug report #24); + affects _parse_hsp_string(). + - Modified Blast::_display_hits() to use table_tiled(), thus + avoiding the buggy Sbjct::_display_hits(). + - Bug fix in Blast::HTML.pm regarding detection of HTML formatting. + - Changes in HSP::_set_data() to support BLAST-GP version 2.0.8. + - Changed the #! line of Bio/Tools/Blast/Run/postclient.pl + to the more standard /usr/bin/perl and predeclared some vars + to avoid compiler warnings. + - blast_config.pl and seqtools.pl were modified to include support + for the -wait option (sets timeout during file/stream reading). + - Assorted touch-ups to example/blast scripts. + +0.073 Mon Dec 28 15:18:29 1998 (bioperl 0.04.2) + - Made changes in Sbjct.pm and HSP.pm to allow parsing of older + versions of Blast. This affected HSP::_set_data() ("Query:?") + and Sbjct::_set_hsps() ("\s*Score"). + - Improved error handling in Sbjct::_set_hsps() and error + detection in HSP_set_data(). + - Added methods for obtaining the number of identical and conserved + residues (sans gaps) sequences in HSP.pm (num_identical, + num_conserved). + - Modified the default behavior of frac_identical() and + frac_conserved() to use the procedure used in the BLAST report: + BLAST-GP: uses total length of alignment in denominator + WU-BLAST: uses length of query sequence (sans gaps) in denominator. + When these methods are called with an argument ('sbjct' or 'query'), + the length of the sbjct or query sequence (sans gaps) is used in + the denominator (recommended). + - Fixed error in test #29 in the t/Blast.t test script. + +0.072 Wed Dec 16 05:05:21 1998 (bioperl 0.04.1) + - Fixed out of range exception in HSP::matches() as suggested by + Michael Lonetto in bio.perl.org bug report #11. + - Made changes in Sbjct.pm and HSP.pm to deal with the reporting of + TBLAST[NX] data in amino acid coordinate space. This affects + frac_identical() and frac_conserved() in HSP.pm, and _tile_hsps(), + length_aln(), frac_aligned_query(), frac_aligned_hit(), + frac_unaligned_query(), frac_unaligned_hit() in Sbjct.pm. + These also in response to bug report #11. + - Fixed behavior of frac_identical() and frac_aligned() in + both Sbjct.pm and HSP.pm to correspond to the data reported + by Blast. Default behavior now includes gaps instead of ignoring + them as before. This was in response to a report by Eli Venter. + - Cleaned up a few "uninitialized value" warnings. + +0.071 Thu Dec 10 18:41:51 1998 (bioperl 0.04) + - Bio::Tools::Blast::Sbjct::_set_id() to no longer uppercases + sequence ids for sbjct sequences. (Note however that the Blast + dataset may have been built with a tool that uppercases all + sequence ids. Check your raw Blast report.). + - Bio::Tools::Blast::HTML.pm incorporates the new URL for + information about the Bioperl Blast module. + +0.07 Thu Dec 3 13:43:06 1998 + - Reduced memory leak that becomes apparent when parsing many Blast + reports. This resulted in changes to Bio::Tools::Blast::_get_parse_func() + and the addition of a new function to Bio::Root::Object.pm that + explicitly breaks cyclic object reference structures. + (This problem was highlighted by recently Lincoln Stein, who is has + created a BoulderIO-based Blast parser. See BoulderIO-1.10 or later). + - Fixed support in blast_config.pl for supplying a custom filtering + function as a string using the -filt_func command-line option. + Added some examples of this to the parse.pl example script. + - Added start() and end() methods to Bio::Tools::Blast::HSP + and Bio::Tools::Blast::Sbjct.pm. Sbjct also received a range() + method (based on discussion with Ewan Birney). + - Fixed bugs in Blast.pm related to accessing the name of the + database, expecially in conjunction with stream parsing. + - A few fixes in Blast.pm and Sbjct regarding handling of + hit sequence and database names (reported by John Calley and + and Karl-Heinz Ott). + - Fixed regexp in Blast::_parse_hsp_data (reported by Brian Karlak). + - Added columns for start/end of the query/sbjct sequences to the + table_tiled() output. Added columns for HSP query/sbjct strand + and frame information to the table() output. + - Changes in Bio::Root::Object.pm regarding strict() and verbose() + which are no longer object-specific. + - Increased documentation in Bio::Root::Object.pm. + - Removed autoloading and several deprecated methods from the + Bio::Root::Object and Utilities. + + +0.062 Fri Sep 4 00:45:05 1998 + - Fixed bugs in Blast::_set_hits() which caused no hits to be + saved when _parse_hsp_data() threw an exception. + - Assorted documentation changes. This includes a fix in + the docs of Bio::Root::Object.pm that caused a compilation error + when you try to use it without installing it via Makefile.PL. + Most modules now have docs for data members in their PODs. + - Added method strip_html() to Bio::Tools::WWW.pm (a more general + version than that found in Bio::Tools::Blast::HTML.pm). + - Includes Bio::Seq.pm version 0.050 (formerly Bio::PreSeq.pm). + This version has Ewan Birney's modifications (start() and end() + methods added; numbering() now deprecated). + - By popular demand, Bio::Root::Object::src_obj() has been changed + to the more intuitive parent(). All modules have been updated to + incorporate this change. + +0.061 Wed Aug 26 12:30:34 1998 + - Fixed memory leak problem associated with Blast::_set_hits() that + lead to excessive memory usage when parsing large numbers reports, + expecially when using the -check_all=>1 parsing option. + (This may have solved the parse_stream.pl memory leak.) + - Fixed regexp in Sbjct::_set_hsps() to recognize sequence lengths + containing commas (reported by Lincoln Stein). + - Blast::signif() now always returns number in scientific notation. + - Fixed bug in Bio::Root::IOManager::display() (wasn't returning true). + - Changed Makefile.PL to always save backups for in-place edits + and prevents the 'inplace edit without backup' warning (reported by + Bobby Otillar). + - Assorted documentation changes/additions. + +0.06 Sun Aug 16 18:31:27 1998 + - Fixed bug in HSP::_set_match_stats() that failed to recognize Frames + on the + strand. + - Added HSP::strand() method for retrieval of strand information for + query and sbjct HSP sequences from nucleotide Blasts. + - Changed calls to Perl's length() function to CORE::length() + to avoid confusing the Perl 5.005_001 interpreter with + Bio::Tools::HSP::length() and Bio::Tools::Sbjct::length(). + (Reported by Mike Cariaso). + - Added column to the output of the Blast::table_tiled() method + to include fraction-aligned of the sbjct sequence. + - Uses new version of Bio::Root::Object.pm that has new exception + handling policy: exceptions and warnings are no longer by default + attached to the objects that threw them. See notes about this in + Bio::Root::Object.pm. (Main reason for 0.003-point jump in version). + - Added some safety net methods in Sbjct.pm: frac_aligned_sbjct() + and num_unaligned_sbjct(), which map to frac_aligned_hit() and + num_unaligned_hit(), respectively (API consistency issue). + - Minor changes/fixes in some of the demo scripts (seqtools.pl et al.). + - Removed "Modifications" notes from Blast-related modules. Added + pointer to distribution site instead, which consolidates this info. + - Modules can be used by copying directly from the lib/ directory into + your perl/lib directory without loss of functionality but at the expense of + increased startup time. It is still recommended that you use the standard + Makefile.PL procedure, however, since this will properly autosplit + the modules as well as run other checks. + +0.057 Thu Jul 23 02:28:26 1998 + - HSP.pm handles "match" sequence lines that are not properly padded. + Affects HSP::_set_data() and other HSP.pm methods that use residue + strings or indices (seq_str(), seq_inds()). (Reported by Libby Shoop). + - Added signif_fmt() method to Blast.pm to allow retrieval of + P/Expect value data in different formats (e.g., exponent only). + - Changes in the table() methods of Blast.pm to accomodate signif_fmt(). + - Minor changes in destructors to improve memory management. + - Added warnings in Blast.pm and parse_stream.pl regarding + memory usage issue when parsing Blast streams. + - Updated HTML::get_html_func() to work with the new version of + Bio::Root::IOManager::read(). + - Added new rexexps to HTML::_markup_report() to deal with hits + which lack a database identifier (e.g., gi|210095). + Added a few other SGD-specific markups to this method. + - New demo script "parse_multi.pl" provided as an alternative to the + memory-hungry parse_stream.pl when crunching many reports. + - Minor changes to parsing demo scripts and blast_config.pl. + - Added more tests to the t/blast.t test script. + - Small change in error handling in Webblast::_blast(): detects + when the Blast report file is empty and unlinks it. + - When the -email option is used, the list of files returned by + blast_remote() contains the string 'email' as the first element. + This provides a signal to Bio::Tools::Blast.pm. + +0.056 Wed Jul 15 03:42:20 1998 + - Fixed bug in HSP::seq_str() in which white space was not removed + from sequences generated by merging multiple lines, leading + to excessive warnings when building Bio::PreSeq objects. + This also involved related fixes in Bio::PreSeq.pm and + Bio::Root::Utilities.pm (q.v.). (Reported by Tim Dudgeon). + - Fixed bug in PreSeq.pm that caused bounds checking to fail + incorrectly when sequence numbering does not begin at 1. + - Uncompressing Blast reports no longer requires write access + in the directory containing the compressed files. + - Added another example script eg/blast/parse2.pl. + - Bio::Root::IOManager::read() now requires the supplied parsing + function reference to return true for each record parsed + (otherwise parsing stops). + +0.055 Tue Jun 23 13:56:34 1998 + - Fixed parsing problems for hit sequences without descriptions + or without database identifiers. This affected + Blast::_parse_hsp_data() and in Sbjct.pm, the methods + _set_id(), _set_desc(), and _set_hsps(). Most seriously, + _set_hsps() failed to locate the 'Length = ' line for + sequences without descriptions. + - Parses parameter data from NCBI Blast 2.0.5 (format change from 2.0.4) + This affected Blast::_set_parameters() and Blast::_parse_hsp_data(). + (Reported by Elliot Lefkowitz.) + - Minor change in HSP::_set_seq() regexp for identifying sequence data. + - Table output methods remove tabs from ends of lines. + - Updated Bio::Tools::Blast::HTML.pm to work with the + new version of read() updated in 0.054. + - Improved file_date() method of Bio::Root::Utilities.pm + +0.054 Tue Jun 16 20:24:36 1998 + - Minor change in the way Bio::Root::IOManager::read() works + (now checks return value of called func ref). Only affects + module internals. + - Minor changes in eg/ scripts and some documentation additions. + - Fixed a bug in Makefile.PL regarding detection of UnivAln.pm. + +0.053 Fri Jun 12 20:55:27 1998 + - Added the "collapse" functionality to the seq_inds() method of + HSP.pm and added a seq_inds() method to Sbjct.pm. + - Added a new demo script eg/blast/parse_positions.pl. + - Remove the "-residues" and "-tile_hsps" parsing options since + they are not necessary. + +0.052 Thu Jun 11 20:18:45 1998 + - Minor bug fixes in I/O methods. + - Improved documentation for Bio::Root modules. + - Miscellaneous documentation additions. + +0.051 Wed Jun 10 12:26:06 1998 + - Bio::Tools::Blast::HSP.pm does some additional deferring of + sequence data processing for a slight performance enhancement. + - Fixed formatting bug in Bio::Tools::Blast::HTML.pm that caused + uneven formatting of some description lines. + - Minor bug fixes in parsing code of Bio::Tools::Blast.pm. + - Some documentation additions. + - Makefile prints warning if Perl version is < 5.003. + +0.05 Fri Jun 5 15:58:22 1998 + - Improved gapped Blast support. + - Enhanced IO (reads from existing file or STDIN). + - Enhanced parsing: can parse an input stream containing + many reports. + - Created modularized version of Alex Dong Li's webblast. + - Added support for running Blasts remotely at NCBI using + Bio::Tools::Blast::Run::Webblast.pm. + - Added support for running local Blasts using the skeletal + Bio::Tools::Blast::Run::LocalBlast.pm. + _ Bio::Tools::Blast::HSP.pm can create Bio::PreSeq.pm sequence + objects and Bio::UnivAln.pm sequence alignment objects on demand. + - Encapsulated HTML-formatting code into the new module + Bio::Tools::Blast::HTML.pm. Updated markup regexps. + - Blast.pm module can parse HTML-formatted reports + (but beware of unforseen changes in the HTML!). + - Enhanced tab-delimited table output methods. + - Improved documentation: compatible with 5.004 pod2html. + - Created a variety of demo scripts (see eg/blast/) + - Miscellaneous bug fixes and API adjustments.. + - Bundled for distribution with MakeMaker and created test sript. + +0.03 Fri Mar 27 23:35:32 1998 + - Support for gapped Blast added. + - Improved parsing strategy. + - Inherits from Bio::Tools::SeqAnal.pm instead of Bio::Root::Object.pm + - Added more documentation. + - Miscellaneous bug fixes. + +0.01 March 1996 + - original version. + - Parses Blast 1.x report files. + + +