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Updated Changes and minor cosmetical edits to blast.t

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1 parent ee6a777 commit a7d7d6f1c0d71c104a41df93ddaae1b144fd6818 @fjossandon fjossandon committed Jan 28, 2014
Showing with 20 additions and 13 deletions.
  1. +8 −1 Changes
  2. +12 −12 t/SearchIO/blast.t
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@@ -50,7 +50,14 @@ CPAN releases are branched from 'master'.
using HMMER outputs and run the full test suite and everything pass [fjossandon]
[Bug fixes]
-
+
+ * Blast: Added support to changes in bl2seq from BLAST+ output, which
+ now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
+ * Phylip: Return undef in "next_aln" at file end to avoid
+ an infinite loop [yschensandiego]
+ * HMMER3: When a hit description is too long, it is truncated in
+ the Scores table. In those cases, the more complete description from
+ the Annotation line (>>) will be used [fjossandon]
* GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
since it is now used by HMMER3 format in alignments [fjossandon]
* GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
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@@ -1522,18 +1522,18 @@ is( $hit->description,
);
is( $hit->length, 606 );
$hsp = $hit->next_hsp;
-is( $hsp->score, 606 );
-is( $hsp->bits, 1120 );
-is( int $hsp->percent_identity, 100 );
-float_is( $hsp->evalue, '0.0' );
-is( $hsp->query->start, 1 );
-is( $hsp->query->end, 606 );
-is( $hsp->query->strand, 1 );
-is( $hsp->hit->strand, 1 );
-is( $hsp->hit->start, 1 );
-is( $hsp->hit->end, 606 );
-is( $hsp->gaps, 0 );
-is( $hsp->n, 1 );
+is( $hsp->score, 606 );
+is( $hsp->bits, 1120 );
+is( $hsp->percent_identity, 100 );
+float_is( $hsp->evalue, '0.0' );
+is( $hsp->query->start, 1 );
+is( $hsp->query->end, 606 );
+is( $hsp->query->strand, 1 );
+is( $hsp->hit->strand, 1 );
+is( $hsp->hit->start, 1 );
+is( $hsp->hit->end, 606 );
+is( $hsp->gaps, 0 );
+is( $hsp->n, 1 );
# this is blastp bl2seq
$searchio = Bio::SearchIO->new(

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