[Bioperl-guts-l] bioperl-live/t entrezgene.t,1.1,1.2

[Stefan Kirov]

Update of /home/repository/bioperl/bioperl-live/t
In directory pub.open-bio.org:/tmp/cvs-serv1931

Modified Files:
	entrezgene.t 
Log Message:
takes care of most warnings...


Index: entrezgene.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/t/entrezgene.t,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** entrezgene.t	16 Jul 2005 00:18:29 -0000	1.1
--- entrezgene.t	16 Jul 2005 22:31:54 -0000	1.2
***************
*** 21,25 ****
      }
  
!     plan tests => ($NUMTESTS = 1006);
  }
  END {
--- 21,25 ----
      }
  
!     plan tests => ($NUMTESTS = 1003);
  }
  END {
***************
*** 149,155 ****
  							 "entrezgene.dat"),-format=>'entrezgene', -debug=>'on',-service_record=>'yes');
  ok $eio;
  while (1) {
  my $seq;
! my ($seq,$struct,$uncapt)=$eio->next_seq;
  last unless ($seq);
  
--- 149,156 ----
  							 "entrezgene.dat"),-format=>'entrezgene', -debug=>'on',-service_record=>'yes');
  ok $eio;
+ my ($seq,$struct,$uncapt);
  while (1) {
  my $seq;
! ($seq,$struct,$uncapt)=$eio->next_seq;
  last unless ($seq);
  
***************
*** 265,269 ****
  my @url=qw(HGMD Ensembl KEGG Homologene);#Only validate the URL
  foreach my $dblink (@dblinks) {
! my $dbname=$dblink->database;
  DB: {
      if ( $dbname eq 'generif') {#Should have ID and text
--- 266,270 ----
  my @url=qw(HGMD Ensembl KEGG Homologene);#Only validate the URL
  foreach my $dblink (@dblinks) {
! my $dbname=$dblink->database||'';
  DB: {
      if ( $dbname eq 'generif') {#Should have ID and text
***************
*** 273,277 ****
      }
      if ($acc==2) {
!         if (($dbname eq 'MIM')&&($dblink->authority eq 'phenotype')) {
              ok $dblink->optional_id;
              last DB;
--- 274,278 ----
      }
      if ($acc==2) {
!         if (($dbname eq 'MIM')&&($dblink->authority)&&($dblink->authority eq 'phenotype')) {
              ok $dblink->optional_id;
              last DB;
***************
*** 352,356 ****
  if (($acc==11305)||($acc==11298)) { #Let's check just this two...
  foreach my $ot ($ann->get_Annotations('OntologyTerm')) {
!     if ($ot->term->authority eq 'STS marker') {
          if ($acc==11305) {
              ok $ot->name,'AI413825';
--- 353,357 ----
  if (($acc==11305)||($acc==11298)) { #Let's check just this two...
  foreach my $ot ($ann->get_Annotations('OntologyTerm')) {
!     if (($ot->term->authority)&&($ot->term->authority eq 'STS marker')) {
          if ($acc==11305) {
              ok $ot->name,'AI413825';
***************
*** 382,391 ****
  
  #T15/16/17: GENOMIC LOCATION TESTS/SEQUENCE TYPES TESTS/CONSERVED DOMAINS TESTS
! my @gffs=('SEQ		gene location	63548355	63556668	.	+	.',
!             'SEQ		genestructure	63548355	63556668	.	+	.',
!             'SEQ		gene location	31124733	31133046	.	+	.',
!             'SEQ		genestructure	31124733	31133046	.	+	.',
!             'SEQ		gene location	8163589	8172398	.	+	.',
!             'SEQ		genestructure	8163589	8172398	.	+	.');
  my @contigs=$struct->get_members;
  my @auth=('mrna','genomic','product','mrna sequence','protein');#Known types....
--- 383,392 ----
  
  #T15/16/17: GENOMIC LOCATION TESTS/SEQUENCE TYPES TESTS/CONSERVED DOMAINS TESTS
! my @gffs=('SEQ	entrezgene	gene location	63548355	63556668	.	+	.',
!             'SEQ	entrezgene	genestructure	63548355	63556668	.	+	.',
!             'SEQ	entrezgene	gene location	31124733	31133046	.	+	.',
!             'SEQ	entrezgene	genestructure	31124733	31133046	.	+	.',
!             'SEQ	entrezgene	gene location	8163589	8172398	.	+	.',
!             'SEQ	entrezgene	genestructure	8163589	8172398	.	+	.');
  my @contigs=$struct->get_members;
  my @auth=('mrna','genomic','product','mrna sequence','protein');#Known types....
***************
*** 396,399 ****
--- 397,401 ----
          if (($contig->authority eq 'genomic')||($contig->authority eq 'Genomic')) {
              foreach my $sf ($contig->get_SeqFeatures) {
+ 		$sf->source_tag('entrezgene');
                  my $gff=$sf->gff_string;
                  $gff=~s/[\t\s]+$//g;