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1 Revision history for Perl extension Bio::Tools::Blast.pm and related modules.
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2
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3 0.091 Thu May 18 15:15:35 2000
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4 (These fixes were made on both branch-06 and the main trunk).
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5 - Fixed Webblast.pm (jitterbug PR #220). It now uses SeqIO and IO::Scalar
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6 for sending formatted query sequence data to the BLAST servers.
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7 - Fixed the examples/blast/ scripts related to remote BLASTing.
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8 - Added single quotes to an '_expect' data member in Sbjct
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9 (reported by Janet Young in jitterbug PR #218).
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10 - Fixed regexp bug in Blast::HTML.pm that caused accessions with
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11 . and _ characters to not be recognized.
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12
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13
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14 0.09 Wed Mar 22 00:44:01 2000
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15 - Handles Blast reports that don't contain description sections.
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16 - Handles parsing of NCBI 2.0.9 Blast2 reports.
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17 - Identifiers of hits are assumed to be the first
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18 chunk of non-whitespace characters in the description line
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19 Does not assume any semantics in the structure of the identifier.
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20 (Blast::Sbjct::_set_id() formerly attempted to extract database
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21 name from the seq identifiers, but this was prone to breaking).
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22 - Fixed bug in the parsing of reports that lack an hits
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23 (incorporated code fix submitted by Michael B. Thornton
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24 jitterbug PR#114, PR#173).
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25 - New helper script retrieve_blast.pl added to examples/blast/
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26 for retrieving Blast reports from NCBI after running
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27 run_blast_remote.pl See docs in retrieve_blast.pl for details.
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28 - Updated Webblast.pm with new URLs for the NCBI servers.
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29 - Fixed bug (jitterbug PR#84) in the parsing of alignments that would
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30 cause occaisionally cause some significant hits to be missed
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31 (incorporates code suggested by Peter van Heusden).
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32 - Added support to Blast.pm for not parsing alignment data
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33 using the new NO_ALIGNS parsing option. Also added -noaligns
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34 command-line option to blast_config.pl (addresses jitterbug PR#93).
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35 - Blast::hit() method doesn't blow up if there are no hits
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36 (fixes jitterbug PR#129).
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37 - Addressed jitterbug PR#96 by correcting docs. If the significance
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38 is defined but of bad format, no default is set.
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39 - HSP.pm properly handles bit scores expressed using floating point
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40 and scientific notation (fixes jitterbug report PR#110).
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41 - Fixed logic error in HSP.pm that would incorrectly throw an
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42 exception when the number of identical residues was zero
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43 (fixes jitterbug PR#164).
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44 - HSP::strand() returns -1, 0, 1 instead of 'Minus', 'Plus', ''
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45 to be in-line with with behavior of SeqFeature.
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46
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47 Fixes within Bio::Root
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48 ----------------------
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49 - Fixed bug reported in PR#85. Bio::Root::Utilities::get_newline()
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50 returns "\n" by default.
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51 - IOManager::read doesn't call alarm() if it isn't available
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52 (fixes bug #PR98).
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53 - Root::Object::_set_io() does not pass @_ to the IOManager constructor
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54 call (incorporates suggestion from Scot Harker, jitterbut PR#192).
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55
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56
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57 0.085 Tue Jun 29 05:15:40 1999 (bioperl 0.05.1)
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58 (Note: the $VERSION variable was not changed to 0.085 in this release!)
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59 - Fixed bugs reported in PR#s: 30, 31, 41, 44, 45, 47, 48
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60 - Blast.pm no longer throws exceptions for hitless reports,
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61 even if a -signif criterion is specified.
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62 - Better support for PSI Blasts (running and parsing) based on
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63 comments/suggestions from Ross Crowhurst and Lu Sun.
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64 - Bug fixes in Webblast.pm regarding blastServerURL and filenames
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65 with special characters (bug reports from James Diggans and
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66 Bradford Powell, respectively).
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67 - Removed =head3 tags that were causing pod2man warnings.
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68 - Fixed -best parsing switch.
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69 - Added better POD to Webblast.pm
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70
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71 0.080 Sat Apr 24 19:39:37 1999 (bioperl 0.05)
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72 - Complete re-implementation of the Blast report parsing strategy.
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73 The parser now always streamifies all Blast report(s) and
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74 segments them hit-wise instead of report-wise. This improves
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75 performance and memory usage (but doesn't solve the memory leak).
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76 - Documented a workaround for the memory leak (see the docs for
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77 Blast.pm under the section "Memory Usage Issues").
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78 - Webblast.pm now uses LWP instead of postclient.pl to post network
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79 Blast requests (thanks to Ross Crowhurst for code submission).
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80 This is a much more robust mechanism, although it now requires you
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81 to have LWP installed ("a good thing"). For example, it makes it
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82 easy to send requests and receive results through a firewall.
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83 It can run Blast1, Blast2, and PSI-Blast at NCBI and also supports
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84 WashU-Blast servers.
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85 - Fixed some miscellaneous parsing bugs and errors reported by
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86 Greg Colello, Xie Tao, and Richard Copley from the pre-release
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87 - Updated example/blast scripts. Renamed parse.pl and parse2.pl to
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88 parse_blast.pl and parse_blast2.pl. parse_stream.pl is gone
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89 (since parse_blast.pl now handles both files and streams).
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90 Renamed run.pl to run_blast_remote.pl and added additional
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91 options to keep it in synch with the new Webblast.pm.
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92
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93
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94 0.075 Wed Feb 17 01:29:57 1999 (bioperl 0.04.4)
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95 - Bug fix in Blast::Run::postclient.pl which was always printing
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96 usage information (reported by Ross Crowhurst).
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97 - Improved error detection & reporting in Blast::Run::Webblast
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98 and Blast::Run::postclient.pl.
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99 - Bug fixes in HSP.pm: _set_match_stats() now properly handles
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100 BLASTN output format and matches() properly handles BLASTX
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101 reports.
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102 - Fixed detection of substitution matrix type in Blast.pm.
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103 - Updated Blast example scripts in examples/blast/
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104 (in particular, run.pl).
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105
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106 0.074 Wed Feb 3 04:10:06 1999 (bioperl 0.04.3)
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107 - Modified blast_config.pl to make the -prog and -db command-line
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108 arguments mandatory. There are no default values for $opt_blast
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109 and $opt_db. Also removed the -dna command-line argument.
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110 - Fixed alignment section parsing bug in Blast.pm (bug report #24);
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111 affects _parse_hsp_string().
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112 - Modified Blast::_display_hits() to use table_tiled(), thus
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113 avoiding the buggy Sbjct::_display_hits().
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114 - Bug fix in Blast::HTML.pm regarding detection of HTML formatting.
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115 - Changes in HSP::_set_data() to support BLAST-GP version 2.0.8.
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116 - Changed the #! line of Bio/Tools/Blast/Run/postclient.pl
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117 to the more standard /usr/bin/perl and predeclared some vars
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118 to avoid compiler warnings.
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119 - blast_config.pl and seqtools.pl were modified to include support
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120 for the -wait option (sets timeout during file/stream reading).
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121 - Assorted touch-ups to example/blast scripts.
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122
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123 0.073 Mon Dec 28 15:18:29 1998 (bioperl 0.04.2)
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124 - Made changes in Sbjct.pm and HSP.pm to allow parsing of older
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125 versions of Blast. This affected HSP::_set_data() ("Query:?")
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126 and Sbjct::_set_hsps() ("\s*Score").
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127 - Improved error handling in Sbjct::_set_hsps() and error
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128 detection in HSP_set_data().
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129 - Added methods for obtaining the number of identical and conserved
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130 residues (sans gaps) sequences in HSP.pm (num_identical,
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131 num_conserved).
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132 - Modified the default behavior of frac_identical() and
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133 frac_conserved() to use the procedure used in the BLAST report:
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134 BLAST-GP: uses total length of alignment in denominator
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135 WU-BLAST: uses length of query sequence (sans gaps) in denominator.
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136 When these methods are called with an argument ('sbjct' or 'query'),
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137 the length of the sbjct or query sequence (sans gaps) is used in
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138 the denominator (recommended).
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139 - Fixed error in test #29 in the t/Blast.t test script.
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140
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141 0.072 Wed Dec 16 05:05:21 1998 (bioperl 0.04.1)
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142 - Fixed out of range exception in HSP::matches() as suggested by
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143 Michael Lonetto in bio.perl.org bug report #11.
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144 - Made changes in Sbjct.pm and HSP.pm to deal with the reporting of
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145 TBLAST[NX] data in amino acid coordinate space. This affects
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146 frac_identical() and frac_conserved() in HSP.pm, and _tile_hsps(),
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147 length_aln(), frac_aligned_query(), frac_aligned_hit(),
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148 frac_unaligned_query(), frac_unaligned_hit() in Sbjct.pm.
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149 These also in response to bug report #11.
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150 - Fixed behavior of frac_identical() and frac_aligned() in
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151 both Sbjct.pm and HSP.pm to correspond to the data reported
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152 by Blast. Default behavior now includes gaps instead of ignoring
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153 them as before. This was in response to a report by Eli Venter.
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154 - Cleaned up a few "uninitialized value" warnings.
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155
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156 0.071 Thu Dec 10 18:41:51 1998 (bioperl 0.04)
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157 - Bio::Tools::Blast::Sbjct::_set_id() to no longer uppercases
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158 sequence ids for sbjct sequences. (Note however that the Blast
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159 dataset may have been built with a tool that uppercases all
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160 sequence ids. Check your raw Blast report.).
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161 - Bio::Tools::Blast::HTML.pm incorporates the new URL for
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162 information about the Bioperl Blast module.
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163
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164 0.07 Thu Dec 3 13:43:06 1998
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165 - Reduced memory leak that becomes apparent when parsing many Blast
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166 reports. This resulted in changes to Bio::Tools::Blast::_get_parse_func()
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167 and the addition of a new function to Bio::Root::Object.pm that
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168 explicitly breaks cyclic object reference structures.
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169 (This problem was highlighted by recently Lincoln Stein, who is has
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170 created a BoulderIO-based Blast parser. See BoulderIO-1.10 or later).
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171 - Fixed support in blast_config.pl for supplying a custom filtering
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172 function as a string using the -filt_func command-line option.
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173 Added some examples of this to the parse.pl example script.
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174 - Added start() and end() methods to Bio::Tools::Blast::HSP
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175 and Bio::Tools::Blast::Sbjct.pm. Sbjct also received a range()
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176 method (based on discussion with Ewan Birney).
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177 - Fixed bugs in Blast.pm related to accessing the name of the
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178 database, expecially in conjunction with stream parsing.
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179 - A few fixes in Blast.pm and Sbjct regarding handling of
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180 hit sequence and database names (reported by John Calley and
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181 and Karl-Heinz Ott).
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182 - Fixed regexp in Blast::_parse_hsp_data (reported by Brian Karlak).
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183 - Added columns for start/end of the query/sbjct sequences to the
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184 table_tiled() output. Added columns for HSP query/sbjct strand
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185 and frame information to the table() output.
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186 - Changes in Bio::Root::Object.pm regarding strict() and verbose()
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187 which are no longer object-specific.
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188 - Increased documentation in Bio::Root::Object.pm.
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189 - Removed autoloading and several deprecated methods from the
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190 Bio::Root::Object and Utilities.
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191
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192
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193 0.062 Fri Sep 4 00:45:05 1998
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194 - Fixed bugs in Blast::_set_hits() which caused no hits to be
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195 saved when _parse_hsp_data() threw an exception.
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196 - Assorted documentation changes. This includes a fix in
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197 the docs of Bio::Root::Object.pm that caused a compilation error
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198 when you try to use it without installing it via Makefile.PL.
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199 Most modules now have docs for data members in their PODs.
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200 - Added method strip_html() to Bio::Tools::WWW.pm (a more general
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201 version than that found in Bio::Tools::Blast::HTML.pm).
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202 - Includes Bio::Seq.pm version 0.050 (formerly Bio::PreSeq.pm).
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203 This version has Ewan Birney's modifications (start() and end()
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204 methods added; numbering() now deprecated).
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205 - By popular demand, Bio::Root::Object::src_obj() has been changed
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206 to the more intuitive parent(). All modules have been updated to
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207 incorporate this change.
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208
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209 0.061 Wed Aug 26 12:30:34 1998
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210 - Fixed memory leak problem associated with Blast::_set_hits() that
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211 lead to excessive memory usage when parsing large numbers reports,
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212 expecially when using the -check_all=>1 parsing option.
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213 (This may have solved the parse_stream.pl memory leak.)
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214 - Fixed regexp in Sbjct::_set_hsps() to recognize sequence lengths
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215 containing commas (reported by Lincoln Stein).
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216 - Blast::signif() now always returns number in scientific notation.
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217 - Fixed bug in Bio::Root::IOManager::display() (wasn't returning true).
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218 - Changed Makefile.PL to always save backups for in-place edits
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219 and prevents the 'inplace edit without backup' warning (reported by
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220 Bobby Otillar).
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221 - Assorted documentation changes/additions.
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222
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223 0.06 Sun Aug 16 18:31:27 1998
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224 - Fixed bug in HSP::_set_match_stats() that failed to recognize Frames
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225 on the + strand.
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226 - Added HSP::strand() method for retrieval of strand information for
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227 query and sbjct HSP sequences from nucleotide Blasts.
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228 - Changed calls to Perl's length() function to CORE::length()
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229 to avoid confusing the Perl 5.005_001 interpreter with
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230 Bio::Tools::HSP::length() and Bio::Tools::Sbjct::length().
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231 (Reported by Mike Cariaso).
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232 - Added column to the output of the Blast::table_tiled() method
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233 to include fraction-aligned of the sbjct sequence.
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234 - Uses new version of Bio::Root::Object.pm that has new exception
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235 handling policy: exceptions and warnings are no longer by default
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236 attached to the objects that threw them. See notes about this in
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237 Bio::Root::Object.pm. (Main reason for 0.003-point jump in version).
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238 - Added some safety net methods in Sbjct.pm: frac_aligned_sbjct()
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239 and num_unaligned_sbjct(), which map to frac_aligned_hit() and
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240 num_unaligned_hit(), respectively (API consistency issue).
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241 - Minor changes/fixes in some of the demo scripts (seqtools.pl et al.).
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242 - Removed "Modifications" notes from Blast-related modules. Added
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243 pointer to distribution site instead, which consolidates this info.
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244 - Modules can be used by copying directly from the lib/ directory into
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245 your perl/lib directory without loss of functionality but at the expense of
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246 increased startup time. It is still recommended that you use the standard
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247 Makefile.PL procedure, however, since this will properly autosplit
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248 the modules as well as run other checks.
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249
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250 0.057 Thu Jul 23 02:28:26 1998
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251 - HSP.pm handles "match" sequence lines that are not properly padded.
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252 Affects HSP::_set_data() and other HSP.pm methods that use residue
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253 strings or indices (seq_str(), seq_inds()). (Reported by Libby Shoop).
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254 - Added signif_fmt() method to Blast.pm to allow retrieval of
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255 P/Expect value data in different formats (e.g., exponent only).
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256 - Changes in the table() methods of Blast.pm to accomodate signif_fmt().
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257 - Minor changes in destructors to improve memory management.
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258 - Added warnings in Blast.pm and parse_stream.pl regarding
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259 memory usage issue when parsing Blast streams.
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260 - Updated HTML::get_html_func() to work with the new version of
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261 Bio::Root::IOManager::read().
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262 - Added new rexexps to HTML::_markup_report() to deal with hits
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263 which lack a database identifier (e.g., gi|210095).
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264 Added a few other SGD-specific markups to this method.
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265 - New demo script "parse_multi.pl" provided as an alternative to the
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266 memory-hungry parse_stream.pl when crunching many reports.
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267 - Minor changes to parsing demo scripts and blast_config.pl.
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268 - Added more tests to the t/blast.t test script.
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269 - Small change in error handling in Webblast::_blast(): detects
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270 when the Blast report file is empty and unlinks it.
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271 - When the -email option is used, the list of files returned by
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272 blast_remote() contains the string 'email' as the first element.
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273 This provides a signal to Bio::Tools::Blast.pm.
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274
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275 0.056 Wed Jul 15 03:42:20 1998
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276 - Fixed bug in HSP::seq_str() in which white space was not removed
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277 from sequences generated by merging multiple lines, leading
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278 to excessive warnings when building Bio::PreSeq objects.
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279 This also involved related fixes in Bio::PreSeq.pm and
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280 Bio::Root::Utilities.pm (q.v.). (Reported by Tim Dudgeon).
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281 - Fixed bug in PreSeq.pm that caused bounds checking to fail
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282 incorrectly when sequence numbering does not begin at 1.
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283 - Uncompressing Blast reports no longer requires write access
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284 in the directory containing the compressed files.
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285 - Added another example script eg/blast/parse2.pl.
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286 - Bio::Root::IOManager::read() now requires the supplied parsing
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287 function reference to return true for each record parsed
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288 (otherwise parsing stops).
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289
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290 0.055 Tue Jun 23 13:56:34 1998
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291 - Fixed parsing problems for hit sequences without descriptions
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292 or without database identifiers. This affected
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293 Blast::_parse_hsp_data() and in Sbjct.pm, the methods
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294 _set_id(), _set_desc(), and _set_hsps(). Most seriously,
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295 _set_hsps() failed to locate the 'Length = ' line for
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296 sequences without descriptions.
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297 - Parses parameter data from NCBI Blast 2.0.5 (format change from 2.0.4)
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298 This affected Blast::_set_parameters() and Blast::_parse_hsp_data().
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299 (Reported by Elliot Lefkowitz.)
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300 - Minor change in HSP::_set_seq() regexp for identifying sequence data.
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301 - Table output methods remove tabs from ends of lines.
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302 - Updated Bio::Tools::Blast::HTML.pm to work with the
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303 new version of read() updated in 0.054.
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304 - Improved file_date() method of Bio::Root::Utilities.pm
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305
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306 0.054 Tue Jun 16 20:24:36 1998
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307 - Minor change in the way Bio::Root::IOManager::read() works
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308 (now checks return value of called func ref). Only affects
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309 module internals.
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310 - Minor changes in eg/ scripts and some documentation additions.
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311 - Fixed a bug in Makefile.PL regarding detection of UnivAln.pm.
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312
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313 0.053 Fri Jun 12 20:55:27 1998
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314 - Added the "collapse" functionality to the seq_inds() method of
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315 HSP.pm and added a seq_inds() method to Sbjct.pm.
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316 - Added a new demo script eg/blast/parse_positions.pl.
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317 - Remove the "-residues" and "-tile_hsps" parsing options since
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318 they are not necessary.
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319
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320 0.052 Thu Jun 11 20:18:45 1998
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321 - Minor bug fixes in I/O methods.
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322 - Improved documentation for Bio::Root modules.
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323 - Miscellaneous documentation additions.
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324
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325 0.051 Wed Jun 10 12:26:06 1998
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326 - Bio::Tools::Blast::HSP.pm does some additional deferring of
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327 sequence data processing for a slight performance enhancement.
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328 - Fixed formatting bug in Bio::Tools::Blast::HTML.pm that caused
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329 uneven formatting of some description lines.
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330 - Minor bug fixes in parsing code of Bio::Tools::Blast.pm.
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331 - Some documentation additions.
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332 - Makefile prints warning if Perl version is < 5.003.
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333
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334 0.05 Fri Jun 5 15:58:22 1998
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335 - Improved gapped Blast support.
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336 - Enhanced IO (reads from existing file or STDIN).
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337 - Enhanced parsing: can parse an input stream containing
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338 many reports.
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339 - Created modularized version of Alex Dong Li's webblast.
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340 - Added support for running Blasts remotely at NCBI using
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341 Bio::Tools::Blast::Run::Webblast.pm.
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342 - Added support for running local Blasts using the skeletal
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343 Bio::Tools::Blast::Run::LocalBlast.pm.
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344 _ Bio::Tools::Blast::HSP.pm can create Bio::PreSeq.pm sequence
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345 objects and Bio::UnivAln.pm sequence alignment objects on demand.
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346 - Encapsulated HTML-formatting code into the new module
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347 Bio::Tools::Blast::HTML.pm. Updated markup regexps.
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348 - Blast.pm module can parse HTML-formatted reports
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349 (but beware of unforseen changes in the HTML!).
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350 - Enhanced tab-delimited table output methods.
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351 - Improved documentation: compatible with 5.004 pod2html.
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352 - Created a variety of demo scripts (see eg/blast/)
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353 - Miscellaneous bug fixes and API adjustments..
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354 - Bundled for distribution with MakeMaker and created test sript.
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355
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356 0.03 Fri Mar 27 23:35:32 1998
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357 - Support for gapped Blast added.
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358 - Improved parsing strategy.
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359 - Inherits from Bio::Tools::SeqAnal.pm instead of Bio::Root::Object.pm
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360 - Added more documentation.
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361 - Miscellaneous bug fixes.
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362
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363 0.01 March 1996
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364 - original version.
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365 - Parses Blast 1.x report files.
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366
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367
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368
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