[Bioperl-guts-l] bioperl-live/t hmmer_pull.t,NONE,1.1.2.1
Senduran Balasubramaniam
sendu at dev.open-bio.org
Sun Aug 20 18:03:32 EDT 2006
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Update of /home/repository/bioperl/bioperl-live/t
In directory dev.open-bio.org:/tmp/cvs-serv10682/t
Added Files:
Tag: branch-1-5-2
hmmer_pull.t
Log Message:
merge from HEAD, bugfixes and new PullParserI and hmmer parser
--- NEW FILE: hmmer_pull.t ---
# -*-Perl-*-
## Bioperl Test Harness Script for Modules
##
# $Id: hmmer_pull.t,v 1.1.2.1 2006/08/20 22:03:30 sendu Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan test => 287;
}
use Bio::Root::IO;
use Bio::SearchIO;
ok(1);
my $searchio = new Bio::SearchIO(-format => 'hmmer_pull', -file => Bio::Root::IO->catfile("t","data","hmmpfam_fake.out"), -verbose => -1);
my @data = ([qw(roa1_drome roa2_drome)], [2, 1], [1, 2], [2, 1]);
while (my $result = $searchio->next_result) {
ok ref($result), 'Bio::Search::Result::HmmpfamResult';
ok $result->algorithm, 'HMMPFAM';
ok $result->algorithm_version, '2.1.1';
ok $result->hmm_name, 'pfam';
ok $result->hmm_file, $result->hmm_name;
ok $result->database_name, $result->hmm_name;
ok $result->sequence_file, '/home/birney/src/wise2/example/road.pep';
ok $result->sequence_database, $result->sequence_file;
ok $result->query_name, shift @{$data[0]};
ok $result->num_hits(), shift @{$data[1]};
ok $result->no_hits_found, 0;
ok $result->query_accession, '';
ok $result->query_description, '';
ok ! $result->query_length;
ok ! $result->database_letters;
ok ! $result->database_entries;
ok $result->algorithm_reference, '';
ok $result->get_parameter('test'), undef;
ok $result->available_parameters, undef;
ok $result->get_statistic('test'), undef;
ok $result->available_statistics, undef;
my @orig_order = $result->hits;
ok @orig_order, shift @{$data[3]};
if (@orig_order > 1) {
ok $orig_order[0]->name ne $orig_order[1]->name;
$result->sort_hits(sub{$Bio::Search::Result::HmmpfamResult::a->[2]
<=>
$Bio::Search::Result::HmmpfamResult::b->[2]});
my @hits = $result->hits;
ok @hits, @orig_order;
ok $hits[0]->name, $orig_order[1]->name;
$result->sort_hits(sub{$Bio::Search::Result::HmmpfamResult::b->[4]
<=>
$Bio::Search::Result::HmmpfamResult::a->[4]});
}
my @hit_data = ([qw(SEED TEST)], [146.1, "5.0"], [6.3e-40, 7.2], [2, 1], [77, undef], [2, 0], [1, 2],
["33 34 36 38 43 45 47 48 51 53 55 57 58 65 68 71 73 74 76 88 98 99 124 125 126 127 129 132 135 140 142 145 146 148 149 151 153 154 156 157 158 159 160 161 164 165 166 167 168 169 170 178 187 189 194", ''],
["1 2 3 4 6 9 11 12 13 15 16 17 19 21 22 23 25 26 28 30 31 33 39 40 41 42 43 44 46 47 48 49 50 51 52 60 61 70 72 73 77", ''],
["1-6 8-13 15-23 25-33 39-56 58-63 67-77", '']);
while (defined(my $hit = $result->next_model)) {
ok ref($hit), 'Bio::Search::Hit::HmmpfamHit';
ok $hit->name, shift @{$hit_data[0]};
ok $hit->raw_score, shift @{$hit_data[1]};
ok $hit->score, $hit->raw_score;
ok $hit->significance, shift @{$hit_data[2]};
ok $hit->p, $hit->significance;
ok $hit->num_hsps, shift @{$hit_data[3]};
ok $hit->n, $hit->num_hsps;
ok $hit->algorithm, $result->algorithm;
ok $hit->overlap, 0;
ok $hit->rank, shift @{$hit_data[6]};
ok $hit->tiled_hsps, 0;
ok $hit->strand('query'), 1;
ok $hit->strand('hit'), 1;
my @strands = $hit->strand;
ok "@strands", "1 1";
ok $hit->description, undef;
ok $hit->accession, undef;
ok ! $hit->locus;
ok ! $hit->bits;
ok ! $result->logical_length('query');
ok ! $result->frame;
ok $hit->each_accession_number, undef;
ok $hit->length, shift @{$hit_data[4]};
ok $hit->logical_length('hit'), $hit->length;
if ($result->query_name eq 'roa1_drome') {
my @inds = $hit->seq_inds('query', 'identical');
ok "@inds", shift @{$hit_data[7]};
@inds = $hit->seq_inds('hit', 'identical');
ok "@inds", shift @{$hit_data[8]};
@inds = $hit->seq_inds('hit', 'conserved', 1);
ok "@inds", shift @{$hit_data[9]};
}
if ($hit->name eq 'SEED') {
my $best = $hit->hsp('best');
ok $best->evalue, 1.1e-18;
my $worst = $hit->hsp('worst');
ok $worst->evalue, 2.2e-17;
ok $hit->start('query'), 33;
ok $hit->start('hit'), 1;
ok $hit->end('query'), 194;
ok $hit->end('hit'), 77;
my @range = $hit->range('query');
ok "@range", '33 194';
@range = $hit->range('hit');
ok "@range", '1 77';
if ($hit->query_name eq 'roa1_drome') {
ok $hit->length_aln('query'),142;
ok $hit->length_aln('hit'), 77;
ok $hit->gaps('total'), 14;
ok $hit->gaps('query'), 13;
ok $hit->gaps('hit'), 1;
ok $hit->matches('id'), 41;
ok $hit->matches('cons'), 24;
ok $hit->frac_identical, 0.387;
ok $hit->frac_conserved, 0.169;
ok ! $hit->frac_aligned_query;
ok $hit->frac_aligned_hit, '1.00';
ok $hit->num_unaligned_hit, 1;
ok $hit->num_unaligned_query, 13;
}
}
my @hsps = $hit->hsps;
ok @hsps, shift @{$hit_data[5]};
my @hsp_data = ([1, 1], [77, 77], [33, 124], [103, 194], [71.2, 75.5], [2.2e-17, 1.1e-18],
['LFIGGLDYRTTDENLKAHFEKWGNIVDVVVMKD-----PRTKRSRGFGFITYSHSSMIDEAQK--SRpHKIDGRVVEP',
'LFVGALKDDHDEQSIRDYFQHFGNIVDINIVID-----KETGKKRGFAFVEFDDYDPVDKVVL-QKQHQLNGKMVDV'],
[7, 6],
['lfVgNLppdvteedLkdlFskfGpivsikivrDiiekpketgkskGfaFVeFeseedAekAlealnG.kelggrklrv',
'lfVgNLppdvteedLkdlFskfGpivsikivrDiiekpketgkskGfaFVeFeseedAekAlealnGkelggrklrv'],
['lf+g+L + +t+e Lk++F+k G iv++ +++D + t++s+Gf+F+++ ++ + A + +++++gr+++ ',
'lfVg L d +e+ ++d+F++fG iv+i+iv+D ketgk +GfaFVeF++++ ++k + ++l+g+ + v'],
[1, 0], [8, 6], [1, 2], ['33 103', '124 194'], [78, 77], [22, 33], [33, 23],
['0.310', '0.465'], ['0.286', '0.429'], ['0.282', '0.429']);
while (defined(my $hsp = $hit->next_domain)) {
ok ref($hsp), 'Bio::Search::HSP::HmmpfamHSP';
ok $hsp->hit->start, shift @{$hsp_data[0]};
ok $hsp->hit->end, shift @{$hsp_data[1]};
ok $hsp->query->start, shift @{$hsp_data[2]};
ok $hsp->query->end, shift @{$hsp_data[3]};
ok $hsp->start('hit'), $hsp->hit->start;
ok $hsp->end('hit'),$hsp->hit->end;
ok $hsp->start('query'), $hsp->query->start;
ok $hsp->end('query'), $hsp->query->end;
ok $hsp->strand('hit'), 1;
ok $hsp->strand('query'), 1;
ok $hsp->score, shift @{$hsp_data[4]};
ok ! $hsp->bits;
ok $hsp->evalue, shift @{$hsp_data[5]};
ok ! $hsp->pvalue;
ok $hsp->significance, $hsp->evalue;
ok $hsp->algorithm, $result->algorithm;
ok $hsp->rank, shift @{$hsp_data[12]};
my @range = $hsp->range;
ok "@range", shift @{$hsp_data[13]};
ok $hsp->n, $hit->num_hsps;
ok $hsp->length('query'), 71;
ok $hsp->length('hit'), 77;
my $locseq = $hsp->seq('hit');
if ($result->query_name eq 'roa1_drome') {
ok ref($locseq), 'Bio::LocatableSeq';
my $aln = $hsp->get_aln('hit');
ok ref($aln), 'Bio::SimpleAlign';
ok $hsp->query_string, shift @{$hsp_data[6]};
ok $hsp->gaps('query'), shift @{$hsp_data[7]};
ok $hsp->gaps('hit'), shift @{$hsp_data[10]};
ok $hsp->gaps('total'), shift @{$hsp_data[11]};
ok $hsp->hit_string, shift @{$hsp_data[8]};
ok $hsp->homology_string, shift @{$hsp_data[9]};
ok $hsp->seq_str('hit'), $hsp->hit_string;
ok $hsp->seq_str('query'), $hsp->query_string;
ok $hsp->seq_str('homology'), $hsp->homology_string;
ok length($hsp->homology_string), length($hsp->hit_string);
ok length($hsp->query_string), length($hsp->homology_string);
ok $hsp->length('total'), shift @{$hsp_data[14]};
ok $hsp->hsp_length, $hsp->length('total');
ok $hsp->num_identical, shift @{$hsp_data[15]};
ok $hsp->num_conserved, shift @{$hsp_data[16]};
ok $hsp->frac_identical('query'), shift @{$hsp_data[17]};
ok $hsp->frac_identical('hit'), shift @{$hsp_data[18]};
ok $hsp->frac_identical('total'), shift @{$hsp_data[19]};
}
}
}
}
ok $searchio->result_count, 2;
- Previous message: [Bioperl-guts-l] bioperl-live/Bio/Search/Result HmmpfamResult.pm, NONE, 1.1.2.1 PullResultI.pm, NONE, 1.1.2.1 GenericResult.pm, 1.23, 1.23.2.1
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