From eb8d5ef0b7e460f7ef70ec513d8a9c428ffc14e3 Mon Sep 17 00:00:00 2001 From: Chris Fields Date: Tue, 19 Feb 2013 09:56:55 -0600 Subject: [PATCH] MUSIGHBA1 no longer works as a primary ID, LOCUS apparently is not indexed; fixing --- Bio/DB/Ace.pm | 18 ++++-------- Bio/DB/GenBank.pm | 24 +++++++-------- Bio/DB/NCBIHelper.pm | 50 ++++++++++++++++---------------- Bio/DB/WebDBSeqI.pm | 82 ++++++++++++++++++++++++++-------------------------- t/RemoteDB/GenBank.t | 36 +++++++++++------------ 5 files changed, 102 insertions(+), 108 deletions(-) diff --git a/Bio/DB/Ace.pm b/Bio/DB/Ace.pm index b6ac12cc8..87dac21e7 100644 --- a/Bio/DB/Ace.pm +++ b/Bio/DB/Ace.pm @@ -2,7 +2,7 @@ # # BioPerl module for Bio::DB::Ace # -# Please direct questions and support issues to +# Please direct questions and support issues to # # Cared for by Ewan Birney # @@ -20,7 +20,7 @@ Bio::DB::Ace - Database object interface to ACeDB servers $db = Bio::DB::Ace->new( -server => 'myace.server.com', port => '120000'); - $seq = $db->get_Seq_by_id('MUSIGHBA1'); # Unique ID + $seq = $db->get_Seq_by_id('J00522'); # Unique ID # or ... @@ -62,15 +62,15 @@ Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists -=head2 Support +=head2 Support Please direct usage questions or support issues to the mailing list: I -rather than to the module maintainer directly. Many experienced and -reponsive experts will be able look at the problem and quickly -address it. Please include a thorough description of the problem +rather than to the module maintainer directly. Many experienced and +reponsive experts will be able look at the problem and quickly +address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs @@ -208,9 +208,3 @@ sub _aceobj { } 1; - - - - - - diff --git a/Bio/DB/GenBank.pm b/Bio/DB/GenBank.pm index d545b0d78..4bf30d17e 100644 --- a/Bio/DB/GenBank.pm +++ b/Bio/DB/GenBank.pm @@ -1,7 +1,7 @@ # # BioPerl module for Bio::DB::GenBank # -# Please direct questions and support issues to +# Please direct questions and support issues to # # Cared for by Aaron Mackey # @@ -10,7 +10,7 @@ # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code -# +# # Added LWP support - Jason Stajich 2000-11-6 # completely reworked by Jason Stajich 2000-12-8 # to use WebDBSeqI @@ -32,7 +32,7 @@ Bio::DB::GenBank - Database object interface to GenBank use Bio::DB::GenBank; $gb = Bio::DB::GenBank->new(); - $seq = $gb->get_Seq_by_id('MUSIGHBA1'); # Unique ID + $seq = $gb->get_Seq_by_id('J00522'); # Unique ID, *not always the LOCUS ID* # or ... @@ -56,11 +56,11 @@ Bio::DB::GenBank - Database object interface to GenBank # also don't want features, just sequence so let's save bandwith # and request Fasta sequence - $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile' , + $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile' , -format => 'Fasta'); my $seqio = $gb->get_Stream_by_acc(['AC013798', 'AC021953'] ); while( my $clone = $seqio->next_seq ) { - print "cloneid is ", $clone->display_id, " ", + print "cloneid is ", $clone->display_id, " ", $clone->accession_number, "\n"; } # note that get_Stream_by_version is not implemented @@ -130,15 +130,15 @@ of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists -=head2 Support +=head2 Support Please direct usage questions or support issues to the mailing list: I -rather than to the module maintainer directly. Many experienced and -reponsive experts will be able look at the problem and quickly -address it. Please include a thorough description of the problem +rather than to the module maintainer directly. Many experienced and +reponsive experts will be able look at the problem and quickly +address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs @@ -169,7 +169,7 @@ use strict; use vars qw(%PARAMSTRING $DEFAULTFORMAT $DEFAULTMODE); use base qw(Bio::DB::NCBIHelper); -BEGIN { +BEGIN { $DEFAULTMODE = 'single'; $DEFAULTFORMAT = 'gbwithparts'; %PARAMSTRING = ( @@ -191,7 +191,7 @@ BEGIN { 'usehistory' => 'n', 'tool' => 'bioperl', 'retmode' => 'text'}, - 'webenv' => { + 'webenv' => { 'query_key' => 'querykey', 'WebEnv' => 'cookie', 'db' => 'nucleotide', @@ -352,7 +352,7 @@ instead. Title : get_request Usage : my $url = $self->get_request Function: HTTP::Request - Returns : + Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc) =cut diff --git a/Bio/DB/NCBIHelper.pm b/Bio/DB/NCBIHelper.pm index 1beb46b67..e9f9d3008 100644 --- a/Bio/DB/NCBIHelper.pm +++ b/Bio/DB/NCBIHelper.pm @@ -1,7 +1,7 @@ # # BioPerl module for Bio::DB::NCBIHelper # -# Please direct questions and support issues to +# Please direct questions and support issues to # # Cared for by Jason Stajich # @@ -10,8 +10,8 @@ # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code -# -# Interfaces with new WebDBSeqI interface +# +# Interfaces with new WebDBSeqI interface =head1 NAME @@ -23,7 +23,7 @@ NCBI databases. # Do not use this module directly. # get a Bio::DB::NCBIHelper object somehow - my $seqio = $db->get_Stream_by_acc(['MUSIGHBA1']); + my $seqio = $db->get_Stream_by_acc(['J00522']); foreach my $seq ( $seqio->next_seq ) { # process seq } @@ -51,15 +51,15 @@ is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists -=head2 Support +=head2 Support Please direct usage questions or support issues to the mailing list: I -rather than to the module maintainer directly. Many experienced and -reponsive experts will be able look at the problem and quickly -address it. Please include a thorough description of the problem +rather than to the module maintainer directly. Many experienced and +reponsive experts will be able look at the problem and quickly +address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs @@ -173,14 +173,14 @@ sub default_format { Title : get_request Usage : my $url = $self->get_request Function: HTTP::Request - Returns : + Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc) =cut sub get_request { my ($self, @qualifiers) = @_; - my ($mode, $uids, $format, $query, $seq_start, $seq_stop, $strand, $complexity) = + my ($mode, $uids, $format, $query, $seq_start, $seq_stop, $strand, $complexity) = $self->_rearrange([qw(MODE UIDS FORMAT QUERY SEQ_START SEQ_STOP STRAND COMPLEXITY)], @qualifiers); $mode = lc $mode; @@ -188,7 +188,7 @@ sub get_request { if( !defined $mode || $mode eq '' ) { $mode = 'single'; } my %params = $self->get_params($mode); if( ! %params ) { - $self->throw("must specify a valid retrieval mode 'single' or 'batch' not '$mode'") + $self->throw("must specify a valid retrieval mode 'single' or 'batch' not '$mode'") } my $url = URI->new($HOSTBASE . $CGILOCATION{$mode}[1]); unless( $mode eq 'webenv' || defined $uids || defined $query) { @@ -258,10 +258,10 @@ NOTE: deprecated API. Use get_Stream_by_id() instead. =cut -*get_Stream_by_batch = sub { +*get_Stream_by_batch = sub { my $self = shift; $self->deprecated('get_Stream_by_batch() is deprecated; use get_Stream_by_id() instead'); - $self->get_Stream_by_id(@_) + $self->get_Stream_by_id(@_) }; =head2 get_Stream_by_query @@ -296,7 +296,7 @@ sub get_Stream_by_query { Function: process downloaded data before loading into a Bio::SeqIO Returns : void Args : hash with two keys - 'type' can be 'string' or 'file' - - 'location' either file location or string + - 'location' either file location or string reference containing data =cut @@ -324,9 +324,9 @@ sub postprocess_data { =cut sub request_format { - my ($self, $value) = @_; + my ($self, $value) = @_; if( defined $value ) { - $value = lc $value; + $value = lc $value; if( defined $FORMATMAP{$value} ) { $self->{'_format'} = [ $value, $FORMATMAP{$value}]; } else { @@ -362,7 +362,7 @@ sub redirect_refseq { Title : complexity Usage : $db->complexity(3) - Function: get/set complexity value + Function: get/set complexity value Returns : value from 0-4 indicating level of complexity Args : value from 0-4 (optional); if unset server assumes 1 Throws : if arg is not an integer or falls outside of noted range above @@ -392,7 +392,7 @@ sub complexity { Title : strand Usage : $db->strand(1) - Function: get/set strand value + Function: get/set strand value Returns : strand value if set Args : value of 1 (plus) or 2 (minus); if unset server assumes 1 Throws : if arg is not an integer or is not 1 or 2 @@ -408,7 +408,7 @@ sub strand { $str !~ /^\d+$/ || $str < 1 || $str > 2; $self->{'_strand'} = $str; } - return $self->{'_strand'}; + return $self->{'_strand'}; } =head2 seq_start @@ -429,7 +429,7 @@ sub seq_start { $start !~ /^\d+$/; $self->{'_seq_start'} = $start; } - return $self->{'_seq_start'}; + return $self->{'_seq_start'}; } =head2 seq_stop @@ -450,7 +450,7 @@ sub seq_stop { $stop !~ /^\d+$/; $self->{'_seq_stop'} = $stop; } - return $self->{'_seq_stop'}; + return $self->{'_seq_stop'}; } =head2 Bio::DB::WebDBSeqI methods @@ -483,8 +483,8 @@ sub get_Stream_by_acc { =head2 _check_id Title : _check_id - Usage : - Function: + Usage : + Function: Returns : A Bio::DB::RefSeq reference or throws Args : $id(s), $string @@ -495,11 +495,11 @@ sub _check_id { # NT contigs can not be retrieved $self->throw("NT_ contigs are whole chromosome files which are not part of regular". - "database distributions. Go to ftp://ftp.ncbi.nih.gov/genomes/.") + "database distributions. Go to ftp://ftp.ncbi.nih.gov/genomes/.") if $ids =~ /NT_/; # Asking for a RefSeq from EMBL/GenBank - + if ($self->redirect_refseq) { if ($ids =~ /N._/) { $self->warn("[$ids] is not a normal sequence database but a RefSeq entry.". diff --git a/Bio/DB/WebDBSeqI.pm b/Bio/DB/WebDBSeqI.pm index 025b789ae..9012c7462 100644 --- a/Bio/DB/WebDBSeqI.pm +++ b/Bio/DB/WebDBSeqI.pm @@ -1,7 +1,7 @@ # # BioPerl module for Bio::DB::WebDBSeqI # -# Please direct questions and support issues to +# Please direct questions and support issues to # # Cared for by Jason Stajich # @@ -10,7 +10,7 @@ # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code -# +# =head1 NAME @@ -47,15 +47,15 @@ is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists -=head2 Support +=head2 Support Please direct usage questions or support issues to the mailing list: I -rather than to the module maintainer directly. Many experienced and -reponsive experts will be able look at the problem and quickly -address it. Please include a thorough description of the problem +rather than to the module maintainer directly. Many experienced and +reponsive experts will be able look at the problem and quickly +address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs @@ -123,17 +123,17 @@ sub new { $ret_type && $self->retrieval_type($ret_type); $delay = $self->delay_policy unless defined $delay; $self->delay($delay); - + # insure we always have a default format set for retrieval # even though this will be immedietly overwritten by most sub classes - $format = $self->default_format unless ( defined $format && + $format = $self->default_format unless ( defined $format && $format ne '' ); $self->request_format($format); my $ua = new LWP::UserAgent(env_proxy => 1); $ua->agent(ref($self) ."/$MODVERSION"); - $self->ua($ua); + $self->ua($ua); $self->{'_authentication'} = []; return $self; } @@ -257,7 +257,7 @@ sub get_Seq_by_version { Title : get_request Usage : my $url = $self->get_request Function: returns a HTTP::Request object - Returns : + Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc) =cut @@ -292,7 +292,7 @@ sub get_Stream_by_id { *get_Stream_by_batch = sub { my $self = shift; $self->deprecated('get_Stream_by_batch() is deprecated; use get_Stream_by_id() instead'); - $self->get_Stream_by_id(@_) + $self->get_Stream_by_id(@_) }; @@ -345,7 +345,7 @@ sub get_Stream_by_gi { sub get_Stream_by_version { my ($self, $ids ) = @_; -# $self->throw("Implementing class should define this method!"); +# $self->throw("Implementing class should define this method!"); return $self->get_seq_stream('-uids' => $ids, '-mode' => 'version'); # how it should work } @@ -356,7 +356,7 @@ sub get_Stream_by_version { Function: Gets a series of Seq objects by way of a query string or oject Returns : a Bio::SeqIO stream object Args : $query : A string that uses the appropriate query language - for the database or a Bio::DB::QueryI object. It is suggested + for the database or a Bio::DB::QueryI object. It is suggested that you create the Bio::DB::Query object first and interrogate it for the entry count before you fetch a potentially large stream. @@ -415,11 +415,11 @@ sub request_format { =head2 get_seq_stream Title : get_seq_stream - Usage : my $seqio = $self->get_seq_sream(%qualifiers) + Usage : my $seqio = $self->get_seq_stream(%qualifiers) Function: builds a url and queries a web db Returns : a Bio::SeqIO stream capable of producing sequence - Args : %qualifiers = a hash qualifiers that the implementing class - will process to make a url suitable for web querying + Args : %qualifiers = a hash qualifiers that the implementing class + will process to make a url suitable for web querying =cut @@ -453,7 +453,7 @@ sub get_seq_stream { if ($self->retrieval_type =~ /pipeline/) { # Try to create a stream using POSIX fork-and-pipe facility. # this is a *big* win when fetching thousands of sequences from - # a web database because we can return the first entry while + # a web database because we can return the first entry while # transmission is still in progress. # Also, no need to keep sequence in memory or in a temporary file. # If this fails (Windows, MacOS 9), we fall back to non-pipelined access. @@ -482,12 +482,12 @@ sub get_seq_stream { my $dir = $self->io->tempdir( CLEANUP => 1); my ( $fh, $tmpfile) = $self->io()->tempfile( DIR => $dir ); close $fh; - my $resp = $self->_request($request, $tmpfile); + my $resp = $self->_request($request, $tmpfile); if( ! -e $tmpfile || -z $tmpfile || ! $resp->is_success() ) { $self->throw("WebDBSeqI Error - check query sequences!\n"); } $self->postprocess_data('type' => 'file', - 'location' => $tmpfile); + 'location' => $tmpfile); # this may get reset when requesting batch mode ($rformat,$ioformat) = $self->request_format(); if( $self->verbose > 0 ) { @@ -505,7 +505,7 @@ sub get_seq_stream { my $content = $resp->content_ref; $self->debug( "content is $$content\n"); if (!$resp->is_success() || length($$content) == 0) { - $self->throw("WebDBSeqI Error - check query sequences!\n"); + $self->throw("WebDBSeqI Error - check query sequences!\n"); } ($rformat,$ioformat) = $self->request_format(); $self->postprocess_data('type'=> 'string', @@ -517,18 +517,18 @@ sub get_seq_stream { } # if we got here, we don't know how to handle the retrieval type - $self->throw("retrieval type " . $self->retrieval_type . + $self->throw("retrieval type " . $self->retrieval_type . " unsupported\n"); } =head2 url_base_address Title : url_base_address - Usage : my $address = $self->url_base_address or + Usage : my $address = $self->url_base_address or $self->url_base_address($address) Function: Get/Set the base URL for the Web Database - Returns : Base URL for the Web Database - Args : $address - URL for the WebDatabase + Returns : Base URL for the Web Database + Args : $address - URL for the WebDatabase =cut @@ -543,7 +543,7 @@ sub url_base_address { =head2 proxy Title : proxy - Usage : $httpproxy = $db->proxy('http') or + Usage : $httpproxy = $db->proxy('http') or $db->proxy(['http','ftp'], 'http://myproxy' ) Function: Get/Set a proxy for use of proxy Returns : a string indicating the proxy @@ -556,9 +556,9 @@ sub url_base_address { sub proxy { my ($self,$protocol,$proxy,$username,$password) = @_; - return if ( !defined $self->ua || !defined $protocol + return if ( !defined $self->ua || !defined $protocol || !defined $proxy ); - $self->authentication($username, $password) + $self->authentication($username, $password) if ($username && $password); return $self->ua->proxy($protocol,$proxy); } @@ -568,7 +568,7 @@ sub proxy { Title : authentication Usage : $db->authentication($user,$pass) Function: Get/Set authentication credentials - Returns : Array of user/pass + Returns : Array of user/pass Args : Array or user/pass @@ -621,8 +621,8 @@ sub retrieval_type { if( defined $value ) { $value = lc $value; if( ! $RETRIEVAL_TYPES{$value} ) { - $self->warn("invalid retrieval type $value must be one of (" . - join(",", keys %RETRIEVAL_TYPES), ")"); + $self->warn("invalid retrieval type $value must be one of (" . + join(",", keys %RETRIEVAL_TYPES), ")"); $value = $DEFAULT_RETRIEVAL_TYPE; } $self->{'_retrieval_type'} = $value; @@ -633,11 +633,11 @@ sub retrieval_type { =head2 url_params Title : url_params - Usage : my $params = $self->url_params or + Usage : my $params = $self->url_params or $self->url_params($params) Function: Get/Set the URL parameters for the Web Database Returns : url parameters for Web Database - Args : $params - parameters to be appended to the URL for the WebDatabase + Args : $params - parameters to be appended to the URL for the WebDatabase =cut @@ -645,13 +645,13 @@ sub url_params { my ($self, $value) = @_; if( defined $value ) { $self->{'_urlparams'} = $value; - } + } } =head2 ua Title : ua - Usage : my $ua = $self->ua or + Usage : my $ua = $self->ua or $self->ua($ua) Function: Get/Set a LWP::UserAgent for use Returns : reference to LWP::UserAgent Object @@ -675,7 +675,7 @@ sub ua { Function: process downloaded data before loading into a Bio::SeqIO Returns : void Args : hash with two keys - 'type' can be 'string' or 'file' - - 'location' either file location or string + - 'location' either file location or string reference containing data =cut @@ -689,12 +689,12 @@ sub postprocess_data { sub _request { my ($self, $url,$tmpfile) = @_; my ($resp); - if( defined $tmpfile && $tmpfile ne '' ) { + if( defined $tmpfile && $tmpfile ne '' ) { $resp = $self->ua->request($url, $tmpfile); - } else { - $resp = $self->ua->request($url); - } - + } else { + $resp = $self->ua->request($url); + } + if( $resp->is_error ) { $self->throw("WebDBSeqI Request Error:\n".$resp->as_string); } @@ -870,7 +870,7 @@ sub mod_perl_api { my $v = $ENV{MOD_PERL} ? ( exists $ENV{MOD_PERL_API_VERSION} && $ENV{MOD_PERL_API_VERSION} >= 2 ) ? 2 : - 1 + 1 : 0; return $v; } diff --git a/t/RemoteDB/GenBank.t b/t/RemoteDB/GenBank.t index ca452799d..0d4d45f65 100755 --- a/t/RemoteDB/GenBank.t +++ b/t/RemoteDB/GenBank.t @@ -6,23 +6,23 @@ use strict; BEGIN { use lib '.'; use Bio::Root::Test; - + test_begin(-tests => 44, -requires_modules => [qw(IO::String LWP::UserAgent HTTP::Request::Common)], -requires_networking => 1); - + use_ok('Bio::DB::GenBank'); } my %expected_lengths = ( - 'MUSIGHBA1' => 408, - 'AF303112' => 1611, - 'AF303112.1' => 1611, - 'AF041456' => 1156, - 'CELRABGDI' => 1743, - 'CH402638' => 5041 + 'MUSIGHBA1' => 408, + 'AF303112' => 1611, + 'AF303112.1' => 1611, + 'AF041456' => 1156, + 'CELRABGDI' => 1743, + 'CH402638' => 5041 ); my ($gb, $seq, $seqio, $seqin); @@ -35,17 +35,17 @@ ok $gb = Bio::DB::GenBank->new('-delay'=>0), 'Bio::DB::GenBank'; # get a single seq SKIP: { - eval {$seq = $gb->get_Seq_by_id('MUSIGHBA1');}; - skip "Couldn't connect to Genbank with Bio::DB::GenBank.pm. Do you have network access? Skipping GenBank tests", 4 if $@; + eval {$seq = $gb->get_Seq_by_id('J00522');1}; + skip "Couldn't connect to Genbank with Bio::DB::GenBank.pm. Do you have network access? Skipping GenBank tests: $@", 4 if $@; is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id; eval {$seq = $gb->get_Seq_by_acc('AF303112');}; - skip "Couldn't connect to Genbank with Bio::DB::GenBank.pm. Transient network problems? Skipping GenBank tests", 3 if $@; + skip "Couldn't connect to Genbank with Bio::DB::GenBank.pm. Transient network problems? Skipping GenBank tests: $@", 3 if $@; is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id; eval {$seq = $gb->get_Seq_by_version('AF303112.1');}; - skip "Couldn't connect to Genbank with Bio::DB::GenBank.pm. Transient network problems? Skipping GenBank tests", 2 if $@; + skip "Couldn't connect to Genbank with Bio::DB::GenBank.pm. Transient network problems? Skipping GenBank tests: $@", 2 if $@; is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id; eval {$seq = $gb->get_Seq_by_gi('405830');}; - skip "Couldn't connect to Genbank with Bio::DB::GenBank.pm. Transient network problems? Skipping GenBank tests", 1 if $@; + skip "Couldn't connect to Genbank with Bio::DB::GenBank.pm. Transient network problems? Skipping GenBank tests: $@", 1 if $@; is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id; } @@ -69,7 +69,7 @@ $seq = $seqio = undef; # test the temporary file creation and fasta ok $gb = Bio::DB::GenBank->new('-format' => 'fasta', '-retrievaltype' => 'tempfile', '-delay' => 0); SKIP: { - eval {$seq = $gb->get_Seq_by_id('MUSIGHBA1');}; + eval {$seq = $gb->get_Seq_by_id('J00522');}; skip "Couldn't connect to complete GenBank tests with a tempfile with Bio::DB::GenBank.pm. Skipping those tests", 6 if $@; # last part of id holds the key is $seq->length, $expected_lengths{(split(/\|/,$seq->display_id))[-1]}, $seq->display_id; @@ -84,7 +84,7 @@ SKIP: { my $done = 0; while (my $s = $seqio->next_seq) { is $s->length, $expected_lengths{$s->display_id}; - undef $gb; # test the case where the db is gone, + undef $gb; # test the case where the db is gone, # but a temp file should remain until seqio goes away. $done++; } @@ -97,7 +97,7 @@ $seq = $seqio = undef; # test pipeline creation ok $gb = Bio::DB::GenBank->new('-retrievaltype' => 'pipeline', '-delay' => 0); SKIP: { - eval {$seq = $gb->get_Seq_by_id('MUSIGHBA1');}; + eval {$seq = $gb->get_Seq_by_id('J00522');}; skip "Couldn't connect to complete GenBank tests with a pipeline with Bio::DB::GenBank.pm. Skipping those tests", 6 if $@; is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id; eval {$seq = $gb->get_Seq_by_acc('AF303112');}; @@ -108,7 +108,7 @@ SKIP: { my $done = 0; while (my $s = $seqio->next_seq) { is $s->length, $expected_lengths{$s->display_id}, $s->display_id; - undef $gb; # test the case where the db is gone, + undef $gb; # test the case where the db is gone, # but the pipeline should remain until seqio goes away $done++; } @@ -150,7 +150,7 @@ SKIP: { is $seq->alphabet, shift(@result); } is @result, 0; - # Real batch retrieval using epost/efetch + # Real batch retrieval using epost/efetch # these tests may change if integrated further into Bio::DB::Gen* # Currently only useful for retrieving GI's via get_seq_stream $gb = Bio::DB::GenBank->new(); -- 2.11.4.GIT