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Fixed test #29 in the Blast.t test script.

svn path=/bioperl-live/branches/release-0-04-bug/; revision=793
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1 parent c89ec7b commit 1d17a1114be6472f96b3430a9a4ea76d4337c1a0 @trutane trutane committed Dec 30, 1998
Showing with 9 additions and 7 deletions.
  1. +5 −3 Bio/Tools/Blast/CHANGES
  2. +4 −4 t/expected.blast.out
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8 Bio/Tools/Blast/CHANGES
@@ -7,14 +7,16 @@ Revision history for Perl extension Bio::Tools::Blast.pm and related modules.
- 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:
+ 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
- Fixed out of range exception in HSP::matches() as suggested by
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8 t/expected.blast.out
@@ -8,9 +8,9 @@ gi|1401126 504 U12856/ATU12856 2000 1.0e-05 124 52 1 0.24 0.43 242 191 6 57 55 2
QUERY Q_LEN SBJCT S_LEN EXPCT SCORE BITS HSPS FR_ID FR_CN FR_ALQ FR_ALS Q_ALN S_ALN Q_GAP S_GAP Q_BEG Q_END S_BEG S_END AMBIG
----- ----- ------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
-gi|1401126 504 U49928/HSU49928 3096 0.0e+00 2580 1009 1 1.00 1.00 1.00 0.16 504 504 0 0 1 504 21 1532 - Homo sapiens TAK1 binding protein (TAB1) mRNA, complete cds
-gi|1401126 504 Z36985/PTPP2CMR 969 4.0e-07 137 57 1 0.25 0.43 0.52 0.23 261 221 2 42 64 324 182 844 - P.tetraurelia mRNA for protein phosphatase type 2C
-gi|1401126 504 X77116/ATMRABI1 1981 1.0e-05 124 52 1 0.24 0.43 0.48 0.10 242 191 6 57 55 296 918 1490 - A.thaliana mRNA for ABI1 protein
-gi|1401126 504 U12856/ATU12856 2000 1.0e-05 124 52 1 0.24 0.43 0.48 0.10 242 191 6 57 55 296 918 1490 - Arabidopsis thaliana Col-0 abscisic acid insensitive protein (ABI1) mRNA, complete cds
+gi|1401126 504 U49928/HSU49928 3096 0.0e+00 2580 1009 1 1.00 1.00 1.00 0.49 504 504 0 0 1 504 21 1532 - Homo sapiens TAK1 binding protein (TAB1) mRNA, complete cds
+gi|1401126 504 Z36985/PTPP2CMR 969 4.0e-07 137 57 1 0.25 0.43 0.52 0.68 261 221 2 42 64 324 182 844 - P.tetraurelia mRNA for protein phosphatase type 2C
+gi|1401126 504 X77116/ATMRABI1 1981 1.0e-05 124 52 1 0.24 0.43 0.48 0.29 242 191 6 57 55 296 918 1490 - A.thaliana mRNA for ABI1 protein
+gi|1401126 504 U12856/ATU12856 2000 1.0e-05 124 52 1 0.24 0.43 0.48 0.29 242 191 6 57 55 296 918 1490 - Arabidopsis thaliana Col-0 abscisic acid insensitive protein (ABI1) mRNA, complete cds

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