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#-*-perl-*-
#$Id$
#testing SoapEUtilities with network queries
# idea: reproduce the examples at
# http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook
use strict;
use warnings;
our $home;
BEGIN {
use Bio::Root::Test;
use lib '.';
$home = '.'; # set to '.' for Build use,
# '..' for debugging from .t file
unshift @INC, $home;
test_begin(-tests => 119,
-requires_modules => [qw(Bio::DB::ESoap
Bio::DB::ESoap::WSDL
Bio::DB::SoapEUtilities
Bio::DB::SoapEUtilities::Result
Bio::DB::SoapEUtilities::FetchAdaptor
Bio::DB::SoapEUtilities::LinkAdaptor
Bio::DB::SoapEUtilities::DocSumAdaptor
SOAP::Lite
XML::Twig
)],
-requires_email => 1);
}
my $dep_msg = "NCBI SOAP EUtilities API no longer supported as of 2015, modules are deprecated and will be removed in a future release";
diag($dep_msg);
SKIP: {
skip($dep_msg, 119);
my $email = test_email();
diag("Using $email for tests") if test_debug();
my ($fac, $result, $seqio, $seq, $i);
my @prot_ids = qw(1621261 89318838 68536103 20807972 730439);
my @prot_ids_2 = qw(828392 790 470338);
my @accns = qw(CAB02640 EAS10332 YP_250808 NP_623143 P41007);
my $lg_contig = 27479347;
my $sciname_id = 527031;
my @gene_ids = qw(828392 790 470338);
my $nbr_test_id = 1621261;
my @linkout_test_ids = qw(28864546 53828898 14523048 14336674 1817575);
SKIP : {
test_skip(-tests => 119,
-requires_networking => 1);
ok $fac = Bio::DB::SoapEUtilities->new(-verbose => test_debug), "SoapEUtilities factory";
diag("Retrieve raw data records from GenBank, save raw data to file, then parse via Bio::SeqIO");
ok $result = $fac->efetch(-email =>$email, -db => 'protein', -id => \@prot_ids_2 )->run(-no_parse=>1), "run efetch, no parse methods";
ok $seqio = Bio::DB::SoapEUtilities::FetchAdaptor->new(-result=>$result), "create adaptor";
for ($i=0; $seq = $seqio->next_seq; $i++) {
isa_ok($seq, 'Bio::Seq::RichSeq');
ok $seq->id, "primary_id present";
1;}
is $i, 3, "iterated all seq objs";
ok $result = $fac->efetch( -rettype => 'fasta' )->run(-no_parse=>1), "run efetch, fasta return, no parse methods";
ok $seqio = Bio::DB::SoapEUtilities::FetchAdaptor->new(-result=>$result), "create adaptor";
for ($i=0; $seq = $seqio->next_seq; $i++) {
isa_ok($seq, 'Bio::Seq');
ok $seq->id, "primary_id present";
1;}
diag("Get accessions (actually accession.versions) for a list of GenBank IDs (GIs)");
# SOAP server doesn't seem to like 'acc' as a rettype, get in fasta format
# and use the result accessors
ok $fac->efetch->set_parameters(-db=>'protein',
-id=>\@prot_ids,
-rettype => 'fasta' ), "set rettype = fasta";
ok $result = $fac->efetch->run, "run query with methods parsing";
is scalar @{$result->TSeqSet_TSeq_TSeqAccver}, 5, "retrieved all accns via \$result->TSeqSet_TSeq_TSeqAccver";
diag("Get GIs for a list of accessions");
ok $fac->efetch->set_parameters( -id=>\@accns ), "set -id to accn list";
ok $result = $fac->efetch->run, "run query with methods parsing";
is scalar @{$result->TSeqSet_TSeq_TSeqGi}, 5, "retrieved all GIs via \$result->TSeqSet_TSeq_TSeqGi";
diag("Downloading a large contig");
ok $fac->efetch->reset_parameters( -db => 'nucleotide',
-email =>$email,
-id => $lg_contig), "set parms for lg contig example";
ok $seqio = $fac->efetch->run( -auto_adapt => 1 ), "run with auto_adapt";
ok $seq = $seqio->next_seq, "iterate adaptor";
ok !$seq->seq, "no sequence present (contig only)";
TODO: {
local $TODO = "why not work with gbwithparts?";
ok $fac->efetch->set_parameters( -rettype=>'gbwithparts' ), "rettype = gbwithparts";
dies_ok { $seqio = $fac->efetch->run( -auto_adapt => 1 ) };
diag("run with auto_adapt (dies not really ok...)");
ok $seq = $seqio->next_seq, "iterate adaptor";
if ($seq) { ok $seq->seq, "sequence now present"; } else {ok 1;}
}
diag("Get the scientific name for an organism");
ok $fac->efetch->reset_parameters( -email =>$email,
-db=>'taxonomy',
-id=>[$sciname_id, $sciname_id+1] ), "set params for sciname test";
ok my $spio = $fac->efetch->run(-auto_adapt => 1), "run with autoadapt";
ok my $sp = $spio->next_species;
like $sp->scientific_name, qr/Bacillus thuringiensis/, "sciname";
is ($sciname_id, $sp->ncbi_taxid, "taxid retrieved and correct");
ok $fac->esummary( -email =>$email, -db => 'taxonomy', -id => $sciname_id ), "set esummary parms";
ok my $docs = $fac->run(-auto_adapt=>1), "run with autoadapt";
ok my $doc = $docs->next_docsum, "iterate adaptor";
like $doc->ScientificName, qr/Bacillus thuringiensis/, "sciname";
is ($sciname_id, $doc->TaxId, "taxid retrieved and correct");
diag("Simple database query");
ok $fac->esearch( -email =>$email, -db=>'protein', -term=> 'BRCA and human', -usehistory=>1 );
ok $result = $fac->run, "run with method parsing";
is $result->QueryTranslation,
'BRCA[All Fields] AND ("Homo sapiens"[Organism] OR human[All Fields])',
"query translation";
cmp_ok $result->count, ">=", 73, "result count";
ok $fac->esearch->reset_parameters(-email =>$email,
-WebEnv => $result->webenv,
-QueryKey => $result->query_key,
-RetMax => 100 );
ok my $wresult = $fac->esearch->run, "run web environment query with retmax set";
cmp_ok $wresult->count, ">=", 73, "all ids retrieved";
diag("What databases are available for querying via eUtils?");
ok $result = $fac->einfo(-email =>$email)->run, "run einfo general query";
cmp_ok scalar(@{$result->dbs}), ">=", 42, "bunch o' dbs";
diag("What information is available for database 'x'?");
ok $result = $fac->einfo(-email =>$email,-db=>'pubmed')->run, "run pubmed info";
is $result->db, 'pubmed', "dbname";
cmp_ok $result->record_count, ">=", 19000000, "record count";
diag("How do I run a global query against all Entrez databases?");
ok my $queries = $fac->egquery(-email =>$email, -term => 'BRCA and human' )->run(-auto_adapt=>1), "run fac for eGQuery, autoadapt";
ok my $query = $queries->query_by_db('protein'), "query by db (protein)";
is $query->term, 'BRCA and human', "term accessor correct";
ok !$queries->query_by_db('bllog'), "no query by db (bllog)";
for ( $i=0; my $q = $queries->next_query; $i++ ) {
ok $q->db, "db (query $i)";
}
cmp_ok scalar($queries->found_in_dbs), ">=", 11, "found in enuf dbs";
cmp_ok scalar($queries->found_in_dbs), "<=", $i, "but not in too many";
diag("I want the document summaries for a list of IDs from database 'x'.");
ok $docs = $fac->esummary(-email =>$email, -db=>'gene', -id=>\@prot_ids_2 )->run(-auto_adapt=>1), "run esummary, autoadapt";
my @tax = (3702, 9606, 9598);
my @acc = qw( NC_003075.7 NC_000002.11 NC_006469.3 );
for ($i=0; my $doc = $docs->next_docsum; $i++) {
is $doc->id, $prot_ids_2[$i], " id retrieved";
is $doc->TaxID, $tax[$i], " taxid retrieved correctly";
is $doc->GenomicInfo->{ChrAccVer}, $acc[$i], "chrom acc/ver retrieved correctly";
cmp_ok scalar ($doc->item_names), ">", 5, "bunch o' items";
}
is $i, 3, "got all docsums";
diag("I want a list of database 'x' UIDs that are linked from a list of database 'y' UIDs");
ok my $links =$fac->elink(-email =>$email,
-db => 'nucleotide',
-dbfrom => 'protein',
-id => \@prot_ids )->run( -auto_adapt => 1),
"run elink protein->nucleotide, auto adapt";
my %h;
for ($i=0; my $linkset = $links->next_linkset; $i++) {
my @ids = $linkset->ids;
my @submitted_ids = $linkset->submitted_ids;
$h{$submitted_ids[0]} = @ids == 1 ? $ids[0] : [@ids];
}
for (keys %h) {
is_deeply( $links->id_map($_) || [], $h{$_}, "id_map correct ($_)");
1;
}
is $i, 5, "got all linksets";
1;
}
}
# remove later
#sub test_input_file { "data/".shift };