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commit 573b3f6b57efdd407229665c51d36c408427eba9 2 parents 3f218f9 + 37eb121
Chris Fields authored
View
18 Bio/DB/Ace.pm
@@ -2,7 +2,7 @@
#
# BioPerl module for Bio::DB::Ace
#
-# Please direct questions and support issues to <bioperl-l@bioperl.org>
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
@@ -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<bioperl-l@bioperl.org>
-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;
-
-
-
-
-
-
View
24 Bio/DB/GenBank.pm
@@ -1,7 +1,7 @@
#
# BioPerl module for Bio::DB::GenBank
#
-# Please direct questions and support issues to <bioperl-l@bioperl.org>
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Aaron Mackey <amackey@virginia.edu>
#
@@ -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<bioperl-l@bioperl.org>
-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
View
50 Bio/DB/NCBIHelper.pm
@@ -1,7 +1,7 @@
#
# BioPerl module for Bio::DB::NCBIHelper
#
-# Please direct questions and support issues to <bioperl-l@bioperl.org>
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# 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<bioperl-l@bioperl.org>
-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.".
View
3  Bio/DB/SeqVersion/gi.pm
@@ -102,6 +102,7 @@ methods. Internal methods are usually preceded with a _
package Bio::DB::SeqVersion::gi;
use strict;
+use Encode;
use HTML::TableExtract;
use base qw(Bio::DB::SeqVersion);
@@ -278,7 +279,7 @@ sub _process_data {
my $te = HTML::TableExtract->new(
headers => ['Gi', 'Version', 'Update Date'] ,
depth => 0);
- $te->parse($html);
+ $te->parse(decode_utf8($html));
my $table = $te->first_table_found;
$self->throw("No table found") unless defined $table;
my $t = [$table->rows];
View
82 Bio/DB/WebDBSeqI.pm
@@ -1,7 +1,7 @@
#
# BioPerl module for Bio::DB::WebDBSeqI
#
-# Please direct questions and support issues to <bioperl-l@bioperl.org>
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
@@ -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<bioperl-l@bioperl.org>
-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;
}
View
18 Bio/Root/Test.pm
@@ -26,7 +26,7 @@ Bio::Root::Test - A common base for all Bioperl test scripts.
my $do_network_tests = test_network();
my $output_debugging = test_debug();
-
+
# Bio::Root::Test rewraps Test::Most, so one can carry out tests with
# Test::More, Test::Exception, Test::Warn, Test::Deep, Test::Diff syntax
@@ -142,12 +142,12 @@ our @ISA = qw(Test::Builder::Module);
{
my $Tester = Test::Builder->new;
-
+
no warnings 'redefine';
sub Test::Warn::_canonical_got_warning {
my ($called_from, $msg) = @_;
my $warn_kind = $called_from eq 'Carp' ? 'carped' : ($called_from =~ /Bio::/ ? 'Bioperl' : 'warn');
-
+
my $warning;
if ($warn_kind eq 'Bioperl') {
($warning) = $msg =~ /\n--------------------- WARNING ---------------------\nMSG: (.+)\n---------------------------------------------------\n$/m;
@@ -157,10 +157,10 @@ our @ISA = qw(Test::Builder::Module);
my @warning_stack = split /\n/, $msg; # some stuff of uplevel is included
$warning = $warning_stack[0];
}
-
+
return {$warn_kind => $warning}; # return only the real message
}
-
+
sub Test::Warn::_diag_found_warning {
foreach (@_) {
if (ref($_) eq 'HASH') {
@@ -173,12 +173,12 @@ our @ISA = qw(Test::Builder::Module);
}
$Tester->diag( "didn't find a warning" ) unless @_;
}
-
+
sub Test::Warn::_cmp_got_to_exp_warning {
my ($got_kind, $got_msg) = %{ shift() };
my ($exp_kind, $exp_msg) = %{ shift() };
return 0 if ($got_kind eq 'warn') && ($exp_kind eq 'carped');
-
+
my $cmp;
if ($got_kind eq 'Bioperl') {
$cmp = $got_msg =~ /^\Q$exp_msg\E$/;
@@ -186,7 +186,7 @@ our @ISA = qw(Test::Builder::Module);
else {
$cmp = $got_msg =~ /^\Q$exp_msg\E at \S+ line \d+\.?$/;
}
-
+
return $cmp;
}
}
@@ -194,7 +194,7 @@ our @ISA = qw(Test::Builder::Module);
our @EXPORT = (@Test::Most::EXPORT,
#@Bio::Root::Test::Warn::EXPORT,
# Test::Warn method wrappers
-
+
# BioPerl-specific
qw(
test_begin
View
2  Bio/SeqIO/chadoxml.pm
@@ -1695,7 +1695,7 @@ sub suppress_residues {
sub allow_residues {
my $self = shift;
- my $allow_residues = shift if defined(@_);
+ my $allow_residues = shift if @_;
return $self->{'allow_residues'} = $allow_residues if defined($allow_residues);
return $self->{'allow_residues'};
}
View
4 examples/db/getGenBank.pl
@@ -14,7 +14,7 @@
my $seqout = new Bio::SeqIO(-fh => \*STDOUT, -format => 'fasta');
# if you want a single seq
-my $seq = $gb->get_Seq_by_id('MUSIGHBA1');
+my $seq = $gb->get_Seq_by_id('J00522');
$seqout->write_seq($seq);
# or by accession
$seq = $gb->get_Seq_by_acc('AF303112');
@@ -23,7 +23,7 @@
# feel free to pull multiple sequences...
# if you want to get a bunch of sequences use the get_Stream_by_id/acc methods
-my $seqio = $gb->get_Stream_by_id([ qw(J00522 AF303112 2981014)]);
+my $seqio = $gb->get_Stream_by_id([ qw(J00522 AF303112 2981014)]);
while( defined ($seq = $seqio->next_seq )) {
$seqout->write_seq($seq);
View
2  t/AlignIO/phylip.t
@@ -85,5 +85,5 @@ TODO: {
# check to see that newlines between header and sequences are parsed correctly
$str = Bio::AlignIO->new('-file' => test_input_file("codeml45b.mlc"), '-format' => 'phylip', '-longid' => 1);
$aln = $str->next_aln();
-my $ls = $aln->get_seq_by_pos(9);
+$ls = $aln->get_seq_by_pos(9);
ok($ls->display_id eq "Pop_trich_ch", "newline between header and sequences is parsed correctly");
View
12 t/Annotation/Annotation.t
@@ -3,12 +3,12 @@
use strict;
-BEGIN {
+BEGIN {
use lib '.';
use Bio::Root::Test;
-
+
test_begin(-tests => 159);
-
+
use_ok('Bio::Annotation::Collection');
use_ok('Bio::Annotation::DBLink');
use_ok('Bio::Annotation::Comment');
@@ -160,7 +160,7 @@ is (scalar($nested_ac->get_Annotations()), 7);
is (scalar($nested_ac->get_all_Annotations()), 7);
SKIP: {
- test_skip(-tests => 7, -requires_modules => [qw(Graph::Directed Bio::Annotation::OntologyTerm)]);
+ test_skip(-tests => 7, -requires_modules => [qw(Bio::Annotation::OntologyTerm)]);
use_ok('Bio::Annotation::OntologyTerm');
# OntologyTerm annotation
my $termann = Bio::Annotation::OntologyTerm->new(-label => 'test case',
@@ -252,7 +252,7 @@ my $ann_tree = Bio::Annotation::Tree->new(
isa_ok($ann_tree, 'Bio::AnnotationI');
$ann_tree->tree_id('test');
is $ann_tree->tree_id(), 'test', "tree_id()";
-$ann_tree->tagname('tree');
+$ann_tree->tagname('tree');
is $ann_tree->tagname(), 'tree', "tagname()";
my $aln_filename = test_input_file('longnames.aln');
use Bio::AlignIO;
@@ -311,7 +311,7 @@ my $ann_struct2 = Bio::Annotation::TagTree->new(-tagname => 'gn',
-value => $val);
is($ann_struct2->value, $val,'roundtrip');
-# formats
+# formats
like($ann_struct2->value, qr/Name: CALM1/,'itext');
$ann_struct2->tagformat('sxpr');
like($ann_struct2->value, qr/\(Name "CALM1"\)/,'spxr');
View
36 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();
View
15 t/RemoteDB/GenPept.t
@@ -6,13 +6,13 @@ use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
-
+
test_begin(-tests => 21,
-requires_modules => [qw(IO::String
LWP::UserAgent
HTTP::Request::Common)],
-requires_networking => 1);
-
+
use_ok('Bio::DB::GenPept');
}
@@ -49,7 +49,7 @@ SKIP: {
$seq = $seqio = undef;
ok $gb = Bio::DB::GenPept->new('-delay' => 0);
-SKIP: {
+SKIP: {
eval {$seq = $gb->get_Seq_by_id('195055');};
skip "Couldn't connect to Genbank with Bio::DB::GenPept.pm. Skipping those tests", 10 if $@;
is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
@@ -65,17 +65,16 @@ SKIP: {
}
skip('No seqs returned', 8) if !$done;
is $done, 2;
- # swissprot genpept parsing
- eval {$seq = $gb->get_Seq_by_acc('2AAA_YEAST');};
+ # swissprot genpept parsing
+ eval {$seq = $gb->get_Seq_by_acc('P31383');};
skip "Couldn't connect to Genbank with Bio::DB::GenPept.pm. Skipping those tests", 5 if $@;
is $seq->length, $expected_lengths{$seq->display_id}, $seq->display_id;
-
+
# test dbsource stuff
# small chance this might change but hopefully not
my @annot = $seq->annotation->get_Annotations('dblink');
- cmp_ok(scalar(@annot), '>', 31);
+ cmp_ok(scalar(@annot), '>', 31);
is $annot[0]->database, 'UniProtKB';
is $annot[0]->primary_id, '2AAA_YEAST';
is (($seq->annotation->get_Annotations('swissprot_dates'))[0]->value, 'Jul 1, 1993');
}
-
View
2  t/RemoteDB/SwissProt.t
@@ -89,7 +89,7 @@ SKIP: {
skip("Problem with idtracker(), skipping these tests: $@", 1) if $@;
cmp_ok(@{$map->{PYRC_YEAST}}, '>=', 2);
- is($map->{PYRC_YEAST}[0], 'CAA30444.1');
+ like($map->{PYRC_YEAST}[0], qr/^[A-Z0-9]/);
}
1;
View
63 t/RemoteDB/Taxonomy.t
@@ -3,10 +3,10 @@
use strict;
-BEGIN {
+BEGIN {
use lib '.';
use Bio::Root::Test;
-
+
test_begin(-tests => 138,
-requires_module => 'XML::Twig');
@@ -53,9 +53,9 @@ for my $db ($db_entrez, $db_flatfile) {
eval { $id = $db->get_taxonid('Homo sapiens');};
skip "Unable to connect to entrez database; no network or server busy?", 38 if $@;
-
+
is $id, 9606;
-
+
# easy test on human, try out the main Taxon methods
ok $n = $db->get_taxon(9606);
is $n->id, 9606;
@@ -63,16 +63,16 @@ for my $db ($db_entrez, $db_flatfile) {
is $n->ncbi_taxid, $n->id;
is $n->parent_id, 9605;
is $n->rank, 'species';
-
+
is $n->node_name, 'Homo sapiens';
is $n->scientific_name, $n->node_name;
is ${$n->name('scientific')}[0], $n->node_name;
-
+
my %common_names = map { $_ => 1 } $n->common_names;
is keys %common_names, 3, ref($db).": common names";
ok exists $common_names{human};
ok exists $common_names{man};
-
+
is $n->division, 'Primates';
is $n->genetic_code, 1;
is $n->mitochondrial_genetic_code, 2;
@@ -82,7 +82,7 @@ for my $db ($db_entrez, $db_flatfile) {
ok defined $n->create_date;
ok defined $n->update_date;
}
-
+
# briefly test some Bio::Tree::NodeI methods
ok my $ancestor = $n->ancestor;
is $ancestor->scientific_name, 'Homo';
@@ -90,13 +90,13 @@ for my $db ($db_entrez, $db_flatfile) {
# each_Descendent; must ask the database directly
ok my @children = $ancestor->db_handle->each_Descendent($ancestor);
cmp_ok @children, '>', 0;
-
+
sleep(3) if $db eq $db_entrez;
-
+
# do some trickier things...
ok my $n2 = $db->get_Taxonomy_Node('89593');
is $n2->scientific_name, 'Craniata';
-
+
# briefly check we can use some Tree methods
my $tree = Bio::Tree::Tree->new();
is $tree->get_lca($n, $n2)->scientific_name, 'Craniata';
@@ -108,36 +108,30 @@ for my $db ($db_entrez, $db_flatfile) {
@lineage_nodes = $tree->get_lineage_nodes($n->id); # read ID, only works if nodes have been added to tree
is scalar @lineage_nodes, 0;
@lineage_nodes = $tree->get_lineage_nodes($n); # node object always works
- is scalar @lineage_nodes, 29;
+ cmp_ok(scalar @lineage_nodes, '>', 20);
# get lineage string
- is $tree->get_lineage_string($n), ($db eq $db_entrez) ?
- 'cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Coelomata;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homo sapiens' :
- 'cellular organisms;Eukaryota;Fungi/Metazoa group;Metazoa;Eumetazoa;Bilateria;Coelomata;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homo/Pan/Gorilla group;Homo;Homo sapiens';
- is $tree->get_lineage_string($n,'-'), ($db eq $db_entrez) ?
- 'cellular organisms-Eukaryota-Opisthokonta-Metazoa-Eumetazoa-Bilateria-Coelomata-Deuterostomia-Chordata-Craniata-Vertebrata-Gnathostomata-Teleostomi-Euteleostomi-Sarcopterygii-Tetrapoda-Amniota-Mammalia-Theria-Eutheria-Euarchontoglires-Primates-Haplorrhini-Simiiformes-Catarrhini-Hominoidea-Hominidae-Homininae-Homo-Homo sapiens' :
- 'cellular organisms-Eukaryota-Fungi/Metazoa group-Metazoa-Eumetazoa-Bilateria-Coelomata-Deuterostomia-Chordata-Craniata-Vertebrata-Gnathostomata-Teleostomi-Euteleostomi-Sarcopterygii-Tetrapoda-Amniota-Mammalia-Theria-Eutheria-Euarchontoglires-Primates-Haplorrhini-Simiiformes-Catarrhini-Hominoidea-Hominidae-Homo/Pan/Gorilla group-Homo-Homo sapiens';
- is $tree->get_lineage_string($n2), ($db eq $db_entrez) ?
- 'cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Coelomata;Deuterostomia;Chordata;Craniata' :
- 'cellular organisms;Eukaryota;Fungi/Metazoa group;Metazoa;Eumetazoa;Bilateria;Coelomata;Deuterostomia;Chordata;Craniata';
-
+ like($tree->get_lineage_string($n), qr/cellular organisms;Eukaryota/);
+ like($tree->get_lineage_string($n,'-'), qr/cellular organisms-Eukaryota/);
+ like($tree->get_lineage_string($n2), qr/cellular organisms;Eukaryota/);
+
# can we actually form a Tree and use other Tree methods?
ok $tree = Bio::Tree::Tree->new(-node => $n);
- is $tree->number_nodes, 30;
- is $tree->get_nodes, 30;
+ cmp_ok($tree->number_nodes, '>', 20);
+ cmp_ok(scalar($tree->get_nodes), '>', 20);
is $tree->find_node(-rank => 'genus')->scientific_name, 'Homo';
-
+
# check that getting the ancestor still works now we have explitly set the
# ancestor by making a Tree
is $n->ancestor->scientific_name, 'Homo';
-
+
sleep(3) if $db eq $db_entrez;
-
+
ok $n = $db->get_Taxonomy_Node('1760');
is $n->scientific_name, 'Actinobacteria';
-
+
sleep(3) if $db eq $db_entrez;
-
+
# entrez isn't as good at searching as flatfile, so we have to special-case
my @ids = sort $db->get_taxonids('Chloroflexi');
is scalar @ids, 2;
@@ -145,7 +139,7 @@ for my $db ($db_entrez, $db_flatfile) {
$id = $db->get_taxonids('Chloroflexi (class)');
$db eq $db_entrez ? is($id, undef) : is($id, 32061);
-
+
@ids = $db->get_taxonids('Rhodotorula');
cmp_ok @ids, '>=' , 8;
@ids = $db->get_taxonids('Rhodotorula <Microbotryomycetidae>');
@@ -213,10 +207,10 @@ SKIP: {
my $h_entrez;
eval { $h_entrez = $db_entrez->get_taxon(-name => 'Homo sapiens');};
skip "Unable to connect to entrez database; no network or server busy?", 5 if $@;
-
+
ok my $tree_functions = Bio::Tree::Tree->new();
is $tree_functions->get_lca($h_flat, $h_entrez)->scientific_name, 'Homo';
-
+
# even though the species taxa for Homo sapiens from list and flat databases
# have the same internal id, get_lca won't work because they have different
# roots and descendents
@@ -239,7 +233,7 @@ for my $name ('Human', 'Hominidae') {
my $ncbi_id = $db_flatfile->get_taxonid($name);
if ($ncbi_id) {
my $node = $db_flatfile->get_taxon(-taxonid => $ncbi_id);
-
+
if ($tree) {
$tree->merge_lineage($node);
}
@@ -258,7 +252,7 @@ SKIP: {
test_skip(-tests => 1, -requires_networking => 1);
eval {$db_entrez->get_taxon(10090);};
skip "Unable to connect to entrez database; no network or server busy?", 1 if $@;
-
+
my $lca = $db_entrez->get_taxon(314146);
my @descs = $db_entrez->get_all_Descendents($lca);
cmp_ok @descs, '>=', 17;
@@ -324,4 +318,3 @@ is $node->ancestor->node_name, 'o__Alteromonadales';
ok $node = $db_list->get_taxon( -names => ['c__Gammaproteobacteria', 'o__Oceanospirillales' , 'f__Alteromonadaceae'] );
is $node->ancestor->node_name, 'o__Oceanospirillales';
-
View
30 t/SeqIO/genbank.t
@@ -6,9 +6,9 @@ use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
-
+
test_begin(-tests => 281 );
-
+
use_ok('Bio::SeqIO::genbank');
}
@@ -392,16 +392,16 @@ my $outfile = test_output_file();
foreach my $in ('BK000016-tpa.gbk', 'ay116458.gb', 'ay149291.gb', 'NC_006346.gb', 'ay007676.gb', 'dq519393.gb') {
my $infile = test_input_file($in);
-
+
$str = Bio::SeqIO->new(-format =>'genbank',
-verbose => $verbose,
-file => $infile);
$seq = $str->next_seq;
-
+
$out = Bio::SeqIO->new(-file => ">$outfile", -format => 'genbank');
$out->write_seq($seq);
$out->close();
-
+
open (IN, $infile);
my @in = <IN>;
close(IN);
@@ -409,7 +409,7 @@ foreach my $in ('BK000016-tpa.gbk', 'ay116458.gb', 'ay149291.gb', 'NC_006346.gb'
my $line = 0;
my $check = 0;
my $is = 1;
-
+
FILECHECK:
while (my $result = <RESULT>) {
if ($result =~ /^KEYWORDS/) {
@@ -422,11 +422,11 @@ foreach my $in ('BK000016-tpa.gbk', 'ay116458.gb', 'ay149291.gb', 'NC_006346.gb'
}
if ($check) {
-
+
# end periods don't count (not all input files have them)
$result =~ s{\.$}{};
$in[$line] =~ s{\.$}{};
-
+
if ($result ne $in[$line]) {
$is = 0;
last;
@@ -434,7 +434,7 @@ foreach my $in ('BK000016-tpa.gbk', 'ay116458.gb', 'ay149291.gb', 'NC_006346.gb'
}
} continue { $line++ }
close(RESULT);
-
+
ok $is, $in;
}
@@ -481,7 +481,7 @@ foreach my $in ('P35527.gb') {
}
ok ( $parts[1], "$parts[0]" );
}
-
+
}
}
}
@@ -489,7 +489,7 @@ foreach my $in ('P35527.gb') {
is($ct, 46);
# bug 2195
-
+
$str = Bio::SeqIO->new(-format =>'genbank',
-verbose => $verbose,
-file => test_input_file('AF305198.gb')
@@ -504,7 +504,7 @@ is(join(', ',$species->classification), 'Virginia creeper phytoplasma, '.
'Firmicutes, Bacteria', 'Bug 2195');
# bug 2569, PROJECT line support, read and write, round-tripping
-
+
$str = Bio::SeqIO->new(-format =>'genbank',
-verbose => $verbose,
-file => test_input_file('NC_008536.gb'));
@@ -573,7 +573,7 @@ is($dblinks[0]->display_text, 'UniProtKB:PYRR_BACSU','operator overloading in An
#bug 2982 embl/genbank contig handling
-$ast = Bio::SeqIO->new( -file => test_input_file('bug2982.gb'),
+$ast = Bio::SeqIO->new( -file => test_input_file('bug2982.gb'),
-format => 'genbank' );
$seq = $ast->next_seq;
@@ -606,8 +606,8 @@ is(scalar @notes, 2);
#bug 3375
my $in = Bio::SeqIO->new(-format => 'genbank',
-file => test_input_file('NC_002058_multDBLINK_bug3375.gb'));
-my $seq = $in->next_seq(); # should not throw a warning now
-my @dblinks = $seq->annotation->get_Annotations('dblink'); # contains 5 dblink references
+$seq = $in->next_seq(); # should not throw a warning now
+@dblinks = $seq->annotation->get_Annotations('dblink'); # contains 5 dblink references
# testing DBLINK BioProject: PRJNA15288
is($dblinks[0]->database, 'BioProject', 'bug3375 database is BioProject');
is($dblinks[0]->primary_id, 'PRJNA15288', 'bug3375 primary_id is PRJNA15288');
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