[Bioperl-guts-l] bioperl-live/t SeqIO.t,1.89,1.90
Brian Osborne
bosborne at pub.open-bio.org
Fri Mar 18 23:11:51 EST 2005
Update of /home/repository/bioperl/bioperl-live/t
In directory pub.open-bio.org:/tmp/cvs-serv21414/t
Modified Files:
SeqIO.t
Log Message:
Add Genbank tests for DBSOURCE line
Index: SeqIO.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/t/SeqIO.t,v
retrieving revision 1.89
retrieving revision 1.90
diff -C2 -d -r1.89 -r1.90
*** SeqIO.t 15 Dec 2004 04:09:00 -0000 1.89
--- SeqIO.t 19 Mar 2005 04:11:48 -0000 1.90
***************
*** 7,35 ****
BEGIN {
! eval { require Test; };
! if( $@ ) {
! use lib 't';
! }
! use Test;
! $TESTCOUNT = 353;
! # interpro uses XML::DOM
! eval {require XML::DOM::XPath};
! if ($@) {
! $TESTCOUNT -= 8;
! $NODOM = 1;
! print STDERR "XML::DOM::XPath not found - skipping interpro tests\n";
! }
! # BSML_SAX uses XML::SAX
! eval {require XML::SAX;
! require XML::SAX::Writer;
! require XML::SAX::Base;
! 1;
};
! if( $@ ) {
! $TESTCOUNT -= 14;
! $NOSAX = 1;
! warn "XML::SAX::Base or XML::SAX or XML::SAX::Writer not found - skipping BSML_SAX tests\n";
! }
! plan tests => $TESTCOUNT;
}
--- 7,35 ----
BEGIN {
! eval { require Test; };
! if( $@ ) {
! use lib 't';
! }
! use Test;
! $TESTCOUNT = 358;
! # interpro uses XML::DOM
! eval {require XML::DOM::XPath};
! if ($@) {
! $TESTCOUNT -= 8;
! $NODOM = 1;
! print STDERR "XML::DOM::XPath not found - skipping interpro tests\n";
! }
! # BSML_SAX uses XML::SAX
! eval {require XML::SAX;
! require XML::SAX::Writer;
! require XML::SAX::Base;
! 1;
};
! if( $@ ) {
! $TESTCOUNT -= 14;
! $NOSAX = 1;
! warn "XML::SAX::Base or XML::SAX or XML::SAX::Writer not found - skipping BSML_SAX tests\n";
! }
! plan tests => $TESTCOUNT;
}
***************
*** 51,80 ****
sub read_write {
! my $format = shift;
! my $seq;
!
! my $str = Bio::SeqIO->new(-file=> Bio::Root::IO->catfile("t","data","test.$format"),
! '-format' => $format);
! ok $seq = $str->next_seq();
! print "Sequence 1 of 2 from $format stream:\n", $seq->seq, "\n\n" if $DEBUG;
!
! unless ($format eq 'raw') {
! ok $seq->id, 'roa1_drome',"ID for format $format";
! ok $seq->length, 358;
! }
! unless ($format eq 'gcg') { # GCG file can contain only one sequence
! ok $seq = $str->next_seq();
! print "Sequence 2 of 2 from $format stream:\n", $seq->seq, $seq->seq, "\n" if $DEBUG;
! }
! my $out = Bio::SeqIO->new('-file'=> ">". Bio::Root::IO->catfile("t","data","$format.out"),
! '-format' => $format);
! ok $out->write_seq($seq);
! if ($format eq 'fasta') {
! my $id_type;
! ok($id_type = $out->preferred_id_type('accession.version'), 'accession.version');
! }
}
--- 51,78 ----
sub read_write {
! my $format = shift;
! my $seq;
! my $str = Bio::SeqIO->new(-file=> Bio::Root::IO->catfile("t","data","test.$format"),
! '-format' => $format);
! ok $seq = $str->next_seq();
! print "Sequence 1 of 2 from $format stream:\n", $seq->seq, "\n\n" if $DEBUG;
! unless ($format eq 'raw') {
! ok $seq->id, 'roa1_drome',"ID for format $format";
! ok $seq->length, 358;
! }
! unless ($format eq 'gcg') { # GCG file can contain only one sequence
! ok $seq = $str->next_seq();
! print "Sequence 2 of 2 from $format stream:\n", $seq->seq, $seq->seq, "\n" if $DEBUG;
! }
+ my $out = Bio::SeqIO->new('-file'=> ">". Bio::Root::IO->catfile("t","data","$format.out"),
+ '-format' => $format);
+ ok $out->write_seq($seq);
+ if ($format eq 'fasta') {
+ my $id_type;
+ ok($id_type = $out->preferred_id_type('accession.version'), 'accession.version');
+ }
}
***************
*** 82,98 ****
foreach my $format (@formats) {
! print "======== $format ========\n" if $DEBUG;
! read_write($format);
}
END {
!
! map { unlink Bio::Root::IO->catfile("t","data","$_.out") } @formats
!
}
my ($str, $seq,$ast,$temp,$mf,$ent,$out); # predeclare variables for strict
- # PIR testing
$str = Bio::SeqIO->new('-file' => Bio::Root::IO->catfile("t","data",
"seqfile.pir"),
--- 80,94 ----
foreach my $format (@formats) {
! print "======== $format ========\n" if $DEBUG;
! read_write($format);
}
END {
! map { unlink Bio::Root::IO->catfile("t","data","$_.out") } @formats
}
my ($str, $seq,$ast,$temp,$mf,$ent,$out); # predeclare variables for strict
+ # PIR testing
$str = Bio::SeqIO->new('-file' => Bio::Root::IO->catfile("t","data",
"seqfile.pir"),
***************
*** 107,110 ****
--- 103,108 ----
}
$out = undef;
+
+ # Genbank
$ast = Bio::SeqIO->new( '-format' => 'GenBank' ,
'-file' => Bio::Root::IO->catfile("t","data",
***************
*** 130,133 ****
--- 128,146 ----
ok(($cds->get_tag_values('transl_except'))[1],
'(pos:complement(4224..4226),aa:OTHER)');
+
+ # This file has a DBSOURCE line, let's see if we can parse it
+ $ast = Bio::SeqIO->new(-format => 'genbank' ,
+ -file => Bio::Root::IO->catfile("t","data",
+ "BAB68554.gb"));
+ $ast->verbose($verbosity);
+ $as = $ast->next_seq();
+ ok $as->molecule, 'linear';
+ ok $as->alphabet, 'protein';
+ ok($as->primary_id, 15824047);
+ my $ac = $as->annotation;
+ ok defined $ac;
+ my @dblinks = $ac->get_Annotations('dblink');
+ ok(scalar @dblinks,1);
+
# embl
$ast = Bio::SeqIO->new( '-format' => 'embl' ,
***************
*** 536,540 ****
my @positions = (
! undef, undef,
undef, undef,
undef, undef,
--- 549,553 ----
my @positions = (
! undef, undef,
undef, undef,
undef, undef,
***************
*** 756,761 ****
-file => Bio::Root::IO->catfile
(qw(t data D12555.gbk)));
! eval {
! $seq = $str->next_seq;
};
--- 769,774 ----
-file => Bio::Root::IO->catfile
(qw(t data D12555.gbk)));
! eval {
! $seq = $str->next_seq;
};
***************
*** 786,810 ****
# test BSML-SAX
! unless( $NOSAX )
! {
! $str = Bio::SeqIO->new(-format => 'bsml_sax',
! -file => Bio::Root::IO->catfile(qw(t data
U83300.bsml) )
! );
! ok($seq = $str->next_seq);
! @refs = $seq->annotation->get_Annotations('reference');
! ok(@refs, 2);
! ok($seq->display_id,'MIVN83300');
! ok($seq->molecule ,'dna');
! ok(! $seq->is_circular);
! ok($seq->get_dates,2);
! ok($seq->accession_number, 'U83300');
! ok($seq->seq_version,1);
! my @feats = $seq->get_SeqFeatures;
! ok(@feats, 2);
! ok($feats[1]->start, 1);
! ok($feats[1]->end, 946);
! ok($feats[1]->get_tag_values('db_xref'), 3);
! ok($seq->annotation->get_Annotations('reference'),2);
! ok($seq->annotation->get_Annotations('dblink'),2);
}
--- 799,822 ----
# test BSML-SAX
! unless( $NOSAX ){
! $str = Bio::SeqIO->new(-format => 'bsml_sax',
! -file => Bio::Root::IO->catfile(qw(t data
U83300.bsml) )
! );
! ok($seq = $str->next_seq);
! @refs = $seq->annotation->get_Annotations('reference');
! ok(@refs, 2);
! ok($seq->display_id,'MIVN83300');
! ok($seq->molecule ,'dna');
! ok(! $seq->is_circular);
! ok($seq->get_dates,2);
! ok($seq->accession_number, 'U83300');
! ok($seq->seq_version,1);
! my @feats = $seq->get_SeqFeatures;
! ok(@feats, 2);
! ok($feats[1]->start, 1);
! ok($feats[1]->end, 946);
! ok($feats[1]->get_tag_values('db_xref'), 3);
! ok($seq->annotation->get_Annotations('reference'),2);
! ok($seq->annotation->get_Annotations('dblink'),2);
}
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