[Bioperl-guts-l] [15032] bioperl-live/trunk/t/blast_pull.t: Redundant; file was renamed SearchIO_blast_pull.t.

Christopher John Fields cjfields at dev.open-bio.org
Wed Nov 26 13:19:45 EST 2008


Revision: 15032
Author:   cjfields
Date:     2008-11-26 13:19:45 -0500 (Wed, 26 Nov 2008)

Log Message:
-----------
Redundant; file was renamed SearchIO_blast_pull.t.

Removed Paths:
-------------
    bioperl-live/trunk/t/blast_pull.t

Deleted: bioperl-live/trunk/t/blast_pull.t
===================================================================
--- bioperl-live/trunk/t/blast_pull.t	2008-11-26 18:09:10 UTC (rev 15031)
+++ bioperl-live/trunk/t/blast_pull.t	2008-11-26 18:19:45 UTC (rev 15032)
@@ -1,413 +0,0 @@
-# -*-Perl-*- Test Harness script for Bioperl
-# $Id$
-
-use strict;
-
-BEGIN {
-	use lib 't/lib';
-    use BioperlTest;
-    
-    test_begin(-tests => 287);
-	
-	use_ok('Bio::SearchIO');
-}
-
-
-my $searchio = Bio::SearchIO->new(-format => 'blast_pull', -file => test_input_file('new_blastn.txt'));
-
-my $result = $searchio->next_result;
-is $result->database_name, 'All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)';
-is $result->database_entries, 3742891;
-is $result->database_letters, 16670205594;
-is $result->algorithm, 'BLASTN';
-is $result->algorithm_version, '2.2.13 [Nov-27-2005]';
-is $result->query_name, 'pyrR,';
-is $result->query_length, 558;
-is $result->get_statistic('kappa'), 0.711;
-is $result->get_statistic('kappa_gapped'), 0.711;
-is $result->get_statistic('lambda'), 1.37;
-is $result->get_statistic('lambda_gapped'), 1.37;
-is $result->get_statistic('entropy'), 1.31;
-is $result->get_statistic('entropy_gapped'), 1.31;
-is $result->get_statistic('dbletters'), -509663586;
-is $result->get_statistic('dbentries'), 3742891;
-is $result->get_statistic('effectivespace'), 8935230198384;
-is $result->get_parameter('matrix'), 'blastn matrix:1 -3';
-is $result->get_parameter('gapopen'), 5;
-is $result->get_parameter('gapext'), 2;
-is $result->get_statistic('S2'), 60;
-is $result->get_statistic('S2_bits'), 119.4;
-is $result->get_parameter('expect'), 1e-23;
-is $result->get_statistic('num_extensions'), 117843;
-
-my @valid = ( [ 'gi|41400296|gb|AE016958.1|', 4829781, 'AE016958', '6e-059', 236],
-	      [ 'gi|54013472|dbj|AP006618.1|', 6021225, 'AP006618', '4e-026', 127],
-	      [ 'gi|57546753|dbj|BA000030.2|', 9025608, 'BA000030', '1e-023', 119]);
-my $count = 0;
-while (my $hit = $result->next_hit ) {
-    my $d = shift @valid;
-
-    is $hit->name, shift @$d;
-    is $hit->length, shift @$d;
-    is $hit->accession, shift @$d;
-    is sprintf("%g",$hit->significance), sprintf("%g",shift @$d);
-    is $hit->raw_score, shift @$d;
-
-    if( $count == 0 ) {
-        my $hsps_left = 1;
-        while( my $hsp = $hit->next_hsp ) {
-            is $hsp->query->start, 262;
-            is $hsp->query->end, 552;
-            is $hsp->hit->start, 1166897;
-            is $hsp->hit->end, 1167187;
-            is $hsp->length('hsp'), 291;
-            is $hsp->start('hit'), $hsp->hit->start;
-            is $hsp->end('query'), $hsp->query->end;
-            is $hsp->strand('sbjct'), $hsp->subject->strand;# alias for hit
-            is $hsp->evalue, 6e-59;
-            is $hsp->score, 119;
-            is $hsp->bits,236;	    	    
-            is sprintf("%.1f",$hsp->percent_identity), 85.2;
-            is sprintf("%.3f",$hsp->frac_identical('query')), 0.852;
-            is sprintf("%.3f",$hsp->frac_identical('hit')), 0.852;
-            is $hsp->gaps, 0;
-            $hsps_left--;
-        }
-        is $hsps_left, 0;
-    }
-    last if( $count++ > @valid );
-}
-is @valid, 0;
-
-# descriptionless hit
-$searchio = Bio::SearchIO->new('-format' => 'blast_pull',
-							   '-file' => test_input_file('blast_no_hit_desc.txt'));
-
-$result = $searchio->next_result;
-my $hit = $result->next_hit;
-is $hit->name, 'chr1';
-is $hit->description, '';
-
-# further (NCBI blastn/p) tests taken from SearchIO.t
-$searchio = Bio::SearchIO->new('-format' => 'blast_pull',
-							   '-file' => test_input_file('ecolitst.bls'));
-
-$result = $searchio->next_result;
-
-is($result->database_name, 'ecoli.aa', 'database_name()');
-is($result->database_entries, 4289);
-is($result->database_letters, 1358990);
-
-is($result->algorithm, 'BLASTP');
-like($result->algorithm_version, qr/^2\.1\.3/);
-like($result->query_name, qr/gi|1786183|gb|AAC73113.1| (AE000111) aspartokinase I,\s+homoserine dehydrogenase I [Escherichia coli]/);
-is($result->query_length, 820);
-is($result->get_statistic('kappa'), '0.135');
-is($result->get_statistic('kappa_gapped'), '0.0410');
-is($result->get_statistic('lambda'), '0.319');
-is($result->get_statistic('lambda_gapped'), '0.267');
-is($result->get_statistic('entropy'), '0.383');
-is($result->get_statistic('entropy_gapped'), '0.140');
-
-is($result->get_statistic('dbletters'), 1358990);
-is($result->get_statistic('dbentries'), 4289);
-is($result->get_statistic('effective_hsplength'), 47);
-is($result->get_statistic('effectivespace'), 894675611);
-is($result->get_parameter('matrix'), 'BLOSUM62');
-is($result->get_parameter('gapopen'), 11);
-is($result->get_parameter('gapext'), 1);
-is($result->get_statistic('S2'), '92');
-is($result->get_statistic('S2_bits'), '40.0');
-is($result->get_parameter('expect'), '1.0e-03');
-is($result->get_statistic('num_extensions'), '82424');
-
-
- at valid = ( [ 'gb|AAC73113.1|', 820, 'AAC73113', '0', 1567],
-	      [ 'gb|AAC76922.1|', 810, 'AAC76922', '1e-91', 332],
-	      [ 'gb|AAC76994.1|', 449, 'AAC76994', '3e-47', 184]);
-$count = 0;
-while (my $hit = $result->next_hit) {
-    my $d = shift @valid;
-
-    is($hit->name, shift @$d);
-    is($hit->length, shift @$d);
-    is($hit->accession, shift @$d);
-    is(sprintf("%g",$hit->significance), sprintf("%g",shift @$d) );
-    is($hit->raw_score, shift @$d );
-
-    if( $count == 0 ) {
-        my $hsps_left = 1;
-        while (my $hsp = $hit->next_hsp) {
-            is($hsp->query->start, 1);
-            is($hsp->query->end, 820);
-            is($hsp->hit->start, 1);
-            is($hsp->hit->end, 820);
-            is($hsp->length('hsp'), 820);
-            is($hsp->start('hit'), $hsp->hit->start);
-            is($hsp->end('query'), $hsp->query->end);
-            is($hsp->strand('sbjct'), $hsp->subject->strand);# alias for hit
-            is($hsp->evalue, '0.0');
-            is($hsp->score, 4058);
-            is($hsp->bits,1567);	    	    
-            is(sprintf("%.2f",$hsp->percent_identity), 98.29);
-            is(sprintf("%.4f",$hsp->frac_identical('query')), 0.9829);
-            is(sprintf("%.4f",$hsp->frac_identical('hit')), 0.9829);
-            is($hsp->gaps, 0);
-            $hsps_left--;
-        }
-        is($hsps_left, 0);
-    }
-    last if( $count++ > @valid );
-}
-is(@valid, 0);
-
-$searchio = Bio::SearchIO->new('-format' => 'blast_pull',
-							  '-file'   => test_input_file('a_thaliana.blastn'));
-
-$result = $searchio->next_result;
-is($result->database_name, 'All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,or phase 0, 1 or 2 HTGS sequences)');
-is($result->database_letters, 4677375331);
-is($result->database_entries, 1083200);
-is($result->algorithm, 'BLASTN');
-like($result->algorithm_version, qr/^2\.2\.1/);
-is($result->query_name, '');
-is($result->query_length, 60);
-is($result->get_parameter('gapopen'), 5);
-is($result->get_parameter('gapext'), 2);
-is($result->get_parameter('ktup'), undef);
-
-is($result->get_statistic('lambda'), 1.37);
-is($result->get_statistic('kappa'), 0.711);
-is($result->get_statistic('entropy'),1.31 );
-is($result->get_statistic('T'), 0);
-is($result->get_statistic('A'), 30);
-is($result->get_statistic('X1'), '6');
-is($result->get_statistic('X1_bits'), 11.9);
-is($result->get_statistic('X2'), 15);
-is($result->get_statistic('X2_bits'), 29.7);
-is($result->get_statistic('S1'), 12);
-is($result->get_statistic('S1_bits'), 24.3);
-is($result->get_statistic('S2'), 17);
-is($result->get_statistic('S2_bits'), 34.2);
-
-is($result->get_statistic('dbentries'), 1083200);
-
- at valid = ( [ 'gb|AY052359.1|', 2826, 'AY052359', '3e-18', 96, 1, 60, 
-	     '1.0000'],
-	   [ 'gb|AC002329.2|AC002329', 76170, 'AC002329', '3e-18', 96, 1, 60, 
-	     '1.0000' ],
-	   [ 'gb|AF132318.1|AF132318', 5383, 'AF132318', '0.04', 42, 35, 55, 
-	     '0.3500']);
-$count = 0;
-
-while( my $hit = $result->next_hit ) {
-    my $d = shift @valid;
-    is($hit->name, shift @$d);
-    is($hit->length, shift @$d);
-    is($hit->accession, shift @$d);
-    is(sprintf("%g",$hit->significance), sprintf("%g",shift @$d) );
-    is($hit->raw_score, shift @$d );
-    is($hit->start, shift @$d);
-    is($hit->end,shift @$d);    
-    is(sprintf("%.4f",$hit->frac_aligned_query), shift @$d);
-    if( $count == 0 ) {
-        my $hsps_left = 1;
-        while( my $hsp = $hit->next_hsp ) {
-            is($hsp->query->start, 1);
-            is($hsp->query->end, 60);
-            is($hsp->query->strand, 1);
-            is($hsp->hit->start, 154);
-            is($hsp->hit->end, 212);
-            is($hsp->hit->strand, 1);
-            is($hsp->length('hsp'), 60);	    
-            is(sprintf("%g",$hsp->evalue), sprintf("%g",'3e-18'));
-            is($hsp->score, 48);
-            is($hsp->bits,95.6);
-            is(sprintf("%.2f",$hsp->percent_identity), 96.67);
-            is(sprintf("%.4f",$hsp->frac_identical('query')), 0.9667);
-            is(sprintf("%.4f",$hsp->frac_identical('hit')), 0.9831);
-            is($hsp->query->frame(), 0);
-            is($hsp->hit->frame(), 0);
-            is($hsp->gaps('query'), 0);
-            is($hsp->gaps('hit'), 1);
-            is($hsp->gaps, 1);	    
-            is($hsp->query_string, 'aggaatgctgtttaattggaatcgtacaatggagaatttgacggaaatagaatcaacgat');
-            is($hsp->hit_string, 'aggaatgctgtttaattggaatca-acaatggagaatttgacggaaatagaatcaacgat');
-            is($hsp->homology_string, '|||||||||||||||||||||||  |||||||||||||||||||||||||||||||||||');
-            is(sprintf("%.2f",$hsp->get_aln->overall_percentage_identity), 96.67);
-            is(sprintf("%.2f",$hsp->get_aln->percentage_identity), 98.31);
-            $hsps_left--;
-        }
-        is($hsps_left, 0);
-    }
-    last if( $count++ > @valid );
-} 
-is(@valid, 0);
-
-$searchio = Bio::SearchIO->new('-format' => 'blast_pull',
-							  '-file'   => test_input_file('frac_problems.blast'));
-my @expected = ("1.000", "0.943");
-while (my $result = $searchio->next_result) {
-    my $hit = $result->next_hit;
-	if (@expected == 2) {
-		is($hit->frac_identical, shift @expected);
-	}
-	else {
-		TODO: {

@@ Diff output truncated at 10000 characters. @@



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