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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: BPlite.t,v 1.20 2002/01/08 09:45:25 birney 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 tests => 97;
}
use Bio::Tools::BPlite;
use Bio::Root::IO;
ok(1);
my $seq =
"MAAQRRSLLQSEQQPSWTDDLPLCHLSGVGSASNRSYSADGKGTESHPPEDSWLKFRSENN".
"CFLYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVERSFLESID".
"DALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMAVVAVLLNNKLYVANV".
"GTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKIKQVGIICGQESTRRIG".
"DYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVTGFLVLMSEGLYKALEAAHGPGQA".
"NQEIAAMIDTEFAKQTSLDAVAQAVVDRVKRIHSDTFASGGERARFCPRHEDMTLLVRNFG".
"YPLGEMSQPTPSPAPAAGGRVYPVSVPYSSAQSTSKTSVTLSLVMPSQGQMVNGAHSASTL".
"DEATPTLTNQSPTLTLQSTNTHTQSSSSSSDGGLFRSRPAHSLPPGEDGRVEPYVDFAEFY".
"RLWSVDHGEQSVVTAP";
open FH, Bio::Root::IO->catfile("t","data","blast.report");
my $report = Bio::Tools::BPlite->new(-fh=>\*FH);
ok $report->isa('Bio::Tools::BPlite');
my $sbjct = $report->nextSbjct;
ok defined $sbjct;
my $hsp = $sbjct->nextHSP;
ok defined $hsp;
ok $report->query, "gi|1401126 (504 letters) ";
ok $report->database, 'Non-redundant GenBank+EMBL+DDBJ+PDB sequences';
ok $sbjct->name, 'gb|U49928|HSU49928 Homo sapiens TAK1 binding protein (TAB1) mRNA, complete cds. ';
ok $hsp->bits, 1009;
ok $hsp->score, 2580;
ok $hsp->percent, 100;
ok $hsp->P, '0.0';
ok $hsp->match, 504;
ok $hsp->positive, 504;
ok $hsp->length, 504;
ok $hsp->querySeq, $seq;
ok $hsp->sbjctSeq, $seq;
ok $hsp->homologySeq, $seq;
ok $hsp->query->start, 1;
ok $hsp->query->end, 504;
ok $hsp->query->seqname, $report->query;
ok $hsp->query->primary_tag, "similarity";
ok $hsp->query->source_tag, "BLAST";
ok $hsp->hit->length, 1512;
ok $hsp->gaps, 0;
$sbjct = $report->nextSbjct;
ok defined $sbjct;
$hsp = $sbjct->nextHSP;
ok defined $hsp;
ok $hsp->bits, 57.8;
ok $hsp->score, 137;
ok int($hsp->percent), 24;
ok ( $hsp->P < 0.00000041 && $hsp->P > 0.00000039);
ok $hsp->match, 64;
ok $hsp->positive, 112;
ok $hsp->hsplength, 261;
ok $hsp->query->start, 64;
ok $hsp->query->end, 324;
ok $hsp->query->length, 261;
ok $hsp->query->seqname, $report->query;
ok $hsp->hit->start, 182;
ok $hsp->hit->end, 844;
ok $hsp->hit->length, 663;
ok $hsp->gaps, 2;
close FH;
# Verify that BPlite is properly parsing PHIBLAST reports as well
my $report2 = Bio::Tools::BPlite->new(-file=>Bio::Root::IO->catfile("t","data","phi.out"));
ok $report2->pattern, "P-E-E-Q";
ok $report2->query_pattern_location->[0], 23;
ok $report2->query_pattern_location->[1], 120;
my $sbjct2 = $report2->nextSbjct;
ok $sbjct2->name =~ /4988/;
my $hsp2 = $sbjct2->nextHSP;
ok $hsp2->hit->end, 343;
close FH;
# test SeqAnalysisParserI
# tests 29-38 are just counting to see that we get the expected number
# of features
my $parser = new Bio::Tools::BPlite(-file => Bio::Root::IO->catfile("t","data","blast.report"));
while( $parser->next_feature ) {
ok(1);
}
$parser = new Bio::Tools::BPlite(-file => Bio::Root::IO->catfile("t","data","cysprot.tblastn"));
while( $parser->next_feature ) {
ok(1);
}
$parser = new Bio::Tools::BPlite(-file => Bio::Root::IO->catfile("t",
"data",
"short.blx"));
ok($parser);
my $count = 0;
while( $parser->next_feature ) {
ok(1);
}
$parser = new Bio::Tools::BPlite(-verbose => 1,
-file => Bio::Root::IO->catfile("t",
"data",
"multiseq.bls"));
ok($parser);
while( my $sbjct = $parser->nextSbjct ) {
while( my $hsp = $sbjct->nextHsp ) {
# some oks would be here, except that this currently does not
# run because multi seq reports are not parsed properly.
}
}
$parser = new Bio::Tools::BPlite(-file => Bio::Root::IO->catfile("t",
"data",
"AE003528_ecoli.bls"));
ok $parser;
ok $parser->qlength, 283821;
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