[Bioperl-guts-l] bioperl-live/Bio/DB/EUtilities efetch.pm, 1.9, 1.10 egquery.pm, 1.7, 1.8 einfo.pm, 1.10, 1.11 elink.pm, 1.26, 1.27 epost.pm, 1.8, 1.9

Wed Sep 20 07:50:10 EDT 2006

Update of /home/repository/bioperl/bioperl-live/Bio/DB/EUtilities
In directory dev.open-bio.org:/tmp/cvs-serv7925/Bio/DB/EUtilities

Modified Files:
	efetch.pm egquery.pm einfo.pm elink.pm epost.pm 
Log Message:
POD cleanup: escape <>

Index: elink.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/EUtilities/elink.pm,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** elink.pm	20 Sep 2006 10:20:01 -0000	1.26
--- elink.pm	20 Sep 2006 11:50:08 -0000	1.27
***************
*** 137,141 ****
  B<PMID> (pubmed), B<MIM number> (omim), B<GI number> (nucleotide, protein),
  B<Genome ID> (genome), B<Popset ID> (popset), B<SNP cluster ID> (snp),
! B<UniSTS ID> (unists), B<UniGene cluster ID> (unigene), <MMDB-ID> (structure),
  B<PSSM-ID> (cdd), B<3D SDI> (domains), B<TAXID> (taxonomy), B<GEO ID> (geo)

--- 137,141 ----
  B<PMID> (pubmed), B<MIM number> (omim), B<GI number> (nucleotide, protein),
  B<Genome ID> (genome), B<Popset ID> (popset), B<SNP cluster ID> (snp),
! B<UniSTS ID> (unists), B<UniGene cluster ID> (unigene), B<MMDB-ID> (structure),
  B<PSSM-ID> (cdd), B<3D SDI> (domains), B<TAXID> (taxonomy), B<GEO ID> (geo)

***************
*** 341,350 ****
  can determine, per ID, what the matching ELink ID is.  The default is to
  return them all as a group (no one-to-one correspondence).  Using a small ID
! array, C<multi_id> set to TRUE, '-id => \@ids', and this loop:

! while (my $linkset = $elink->next_linkset) {
      print "Query ID : ",join q(,), $linkset->query_id,"\n";
      print "\tTax ID : ",join q(,), $linkset->get_LinkIds_by_db('taxonomy'),"\n";
! }

  gets this result:
--- 341,350 ----
  can determine, per ID, what the matching ELink ID is.  The default is to
  return them all as a group (no one-to-one correspondence).  Using a small ID
! array, C<multi_id> set to TRUE, '-id =E<gt> \@ids', and this loop:

!   while (my $linkset = $elink->next_linkset) {
      print "Query ID : ",join q(,), $linkset->query_id,"\n";
      print "\tTax ID : ",join q(,), $linkset->get_LinkIds_by_db('taxonomy'),"\n";
!   }

  gets this result:

Index: einfo.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/EUtilities/einfo.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** einfo.pm	6 Sep 2006 05:36:41 -0000	1.10
--- einfo.pm	20 Sep 2006 11:50:08 -0000	1.11
***************
*** 19,28 ****
  =head1 SYNOPSIS

! my $einfo = Bio::DB::EUtilities->new(
                                       -eutil    => 'einfo',
                                       -db       => 'pubmed'
                                        );

! print $einfo->get_response->content;

  =head1 DESCRIPTION
--- 19,28 ----
  =head1 SYNOPSIS

!   my $einfo = Bio::DB::EUtilities->new(
                                       -eutil    => 'einfo',
                                       -db       => 'pubmed'
                                        );

!   print $einfo->get_response->content;

  =head1 DESCRIPTION
***************
*** 66,70 ****
    bioperl-l at lists.open-bio.org               - General discussion
    http://www.bioperl.org/wiki/Mailing_lists  - About the mailing lists
!   
  =head2 Reporting Bugs

--- 66,70 ----
    bioperl-l at lists.open-bio.org               - General discussion
    http://www.bioperl.org/wiki/Mailing_lists  - About the mailing lists
! 
  =head2 Reporting Bugs

Index: epost.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/EUtilities/epost.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** epost.pm	20 Sep 2006 10:20:01 -0000	1.8
--- epost.pm	20 Sep 2006 11:50:08 -0000	1.9
***************
*** 70,75 ****
  Below are a list of IDs which can be used with EPost:

! B<PMID> (pubmed), <MEDLINE UI> (NIH MedLine), B<MIM number> (omim),
! B<GI number> (nucleotide, protein), <MMDB-ID> (structure),B<TAXID> (taxonomy)

  =back
--- 70,75 ----
  Below are a list of IDs which can be used with EPost:

! B<PMID> (pubmed), B<MEDLINE UI> (NIH MedLine), B<MIM number> (omim),
! B<GI number> (nucleotide, protein), B<MMDB-ID> (structure), B<TAXID> (taxonomy)

  =back

Index: efetch.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/EUtilities/efetch.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** efetch.pm	20 Sep 2006 10:20:01 -0000	1.9
--- efetch.pm	20 Sep 2006 11:50:08 -0000	1.10
***************
*** 71,75 ****
  B<PMID> (pubmed), B<MIM number> (omim), B<GI number> (nucleotide, protein),
  B<Genome ID> (genome), B<Popset ID> (popset), B<SNP cluster ID> (snp),
! B<UniSTS ID> (unists), B<UniGene cluster ID> (unigene), <MMDB-ID> (structure),
  B<PSSM-ID> (cdd), B<3D SDI> (domains), B<TAXID> (taxonomy), B<GEO ID> (geo)

--- 71,75 ----
  B<PMID> (pubmed), B<MIM number> (omim), B<GI number> (nucleotide, protein),
  B<Genome ID> (genome), B<Popset ID> (popset), B<SNP cluster ID> (snp),
! B<UniSTS ID> (unists), B<UniGene cluster ID> (unigene), B<MMDB-ID> (structure),
  B<PSSM-ID> (cdd), B<3D SDI> (domains), B<TAXID> (taxonomy), B<GEO ID> (geo)

Index: egquery.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/EUtilities/egquery.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** egquery.pm	20 Sep 2006 10:20:01 -0000	1.7
--- egquery.pm	20 Sep 2006 11:50:08 -0000	1.8
***************
*** 19,28 ****
  =head1 SYNOPSIS

! my $egquery = Bio::DB::EUtilities->new(
                                       -eutil    => 'egquery',
                                       -term     => 'dihydroorotase'
                                        );

! print $egquery->get_response->content;

  =head1 DESCRIPTION
--- 19,28 ----
  =head1 SYNOPSIS

!     my $egquery = Bio::DB::EUtilities->new(
                                       -eutil    => 'egquery',
                                       -term     => 'dihydroorotase'
                                        );

!     print $egquery->get_response->content;

  =head1 DESCRIPTION