From f28077eb3d77fa51474b770c1ca7b045cb7e45dc Mon Sep 17 00:00:00 2001 From: "Francisco J. Ossandon" Date: Fri, 7 Nov 2014 18:24:45 -0300 Subject: [PATCH] Change EMBL entry name (BUM) that is not working for other that currently works (HSFOS) --- Bio/DB/BioFetch.pm | 4 ++-- Bio/DB/EMBL.pm | 2 +- Bio/DB/Flat.pm | 4 ++-- examples/db/dbfetch | 4 ++-- scripts/DB/bp_biofetch_genbank_proxy.pl | 2 +- t/Perl.t | 2 +- 6 files changed, 9 insertions(+), 9 deletions(-) diff --git a/Bio/DB/BioFetch.pm b/Bio/DB/BioFetch.pm index 4ac5740b8..bdf4b3582 100644 --- a/Bio/DB/BioFetch.pm +++ b/Bio/DB/BioFetch.pm @@ -26,14 +26,14 @@ Bio::DB::BioFetch - Database object interface to BioFetch retrieval $bf = Bio::DB::BioFetch->new(); - $seq = $bf->get_Seq_by_id('BUM'); # EMBL or SWALL ID + $seq = $bf->get_Seq_by_id('HSFOS'); # EMBL or SWALL ID # change formats, storage procedures $bf = Bio::DB::BioFetch->new(-format => 'fasta', -retrievaltype => 'tempfile', -db => 'EMBL'); - $stream = $bf->get_Stream_by_id(['BUM','J00231']); + $stream = $bf->get_Stream_by_id(['HSFOS','J00231']); while (my $s = $stream->next_seq) { print $s->seq,"\n"; } diff --git a/Bio/DB/EMBL.pm b/Bio/DB/EMBL.pm index 4d187115f..3b1fb3f1b 100644 --- a/Bio/DB/EMBL.pm +++ b/Bio/DB/EMBL.pm @@ -23,7 +23,7 @@ Bio::DB::EMBL - Database object interface for EMBL entry retrieval $embl = Bio::DB::EMBL->new(); # remember that EMBL_ID does not equal GenBank_ID! - $seq = $embl->get_Seq_by_id('BUM'); # EMBL ID + $seq = $embl->get_Seq_by_id('HSFOS'); # EMBL ID print "cloneid is ", $seq->id, "\n"; # or changeing to accession number and Fasta format ... diff --git a/Bio/DB/Flat.pm b/Bio/DB/Flat.pm index a911ed5a6..f285227ff 100644 --- a/Bio/DB/Flat.pm +++ b/Bio/DB/Flat.pm @@ -23,9 +23,9 @@ Bio::DB::Flat - Interface for indexed flat files -write_flag => 1); $db->build_index('/usr/share/embl/primate.embl', '/usr/share/embl/protists.embl'); - $seq = $db->get_Seq_by_id('BUM'); + $seq = $db->get_Seq_by_id('HSFOS'); @sequences = $db->get_Seq_by_acc('DIV' => 'primate'); - $raw = $db->fetch_raw('BUM'); + $raw = $db->fetch_raw('HSFOS'); =head1 DESCRIPTION diff --git a/examples/db/dbfetch b/examples/db/dbfetch index cb6d69ed5..b0dc7458a 100755 --- a/examples/db/dbfetch +++ b/examples/db/dbfetch @@ -39,7 +39,7 @@ searches returning more than one entry per query term are not in these specs. In its default setup, type one or more EMBL accession numbers -(e.g. J00231), entry name (e.g. BUM) or sequence version into the +(e.g. J00231), entry name (e.g. HSFOS) or sequence version into the seach dialog to retieve hypertext linked enties. Note that for practical reasons only the first 50 identifiers @@ -276,7 +276,7 @@ sub print_prompt { $q->p("This page allows you to retrieve up to ". MAXIDS . " entries at the time from various up-to-date biological databases."), $q->p("For EMBL, enter an accession number (e.g. J00231) or entry name (e.g. - BUM) or a sequence version (e.g. J00231.1), or any combination of them + HSFOS) or a sequence version (e.g. J00231.1), or any combination of them separated by a non-word character into your browser's search dialog. SWALL examples are: fos_human, p53_human. For short Ensembl entries, try : AL122059, AL031002, AL031030 . diff --git a/scripts/DB/bp_biofetch_genbank_proxy.pl b/scripts/DB/bp_biofetch_genbank_proxy.pl index 05deac528..1275c91d3 100644 --- a/scripts/DB/bp_biofetch_genbank_proxy.pl +++ b/scripts/DB/bp_biofetch_genbank_proxy.pl @@ -184,7 +184,7 @@ option: id Option : id Descr : unique database identifier(s) Type : required - Usage : db=J00231 | id=J00231+BUM + Usage : db=J00231 | id=J00231+HSFOS Arg : string The ID option should be able to process all UIDS in a database. It diff --git a/t/Perl.t b/t/Perl.t index 8c2d20cf6..38055b23b 100644 --- a/t/Perl.t +++ b/t/Perl.t @@ -81,7 +81,7 @@ SKIP: { # embl SKIP: { eval { - $seq_object = get_sequence('embl',"BUM"); + $seq_object = get_sequence('embl',"HSFOS"); }; if ($@) { skip("problem connecting to EMBL:$@",2); -- 2.11.4.GIT