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Propagated leftover changes from v1.6.x

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commit da82f48fb0e8dc635681524fe4851522d2f89a97 1 parent adebb79
@fjossandon fjossandon authored
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4 Bio/DB/GenBank.pm
@@ -173,7 +173,7 @@ BEGIN {
$DEFAULTMODE = 'single';
$DEFAULTFORMAT = 'gbwithparts';
%PARAMSTRING = (
- 'batch' => { 'db' => 'nucleotide',
+ 'batch' => { 'db' => 'nucleotide',
'usehistory' => 'n',
'tool' => 'bioperl'},
'query' => { 'usehistory' => 'y',
@@ -191,7 +191,7 @@ BEGIN {
'usehistory' => 'n',
'tool' => 'bioperl',
'retmode' => 'text'},
- 'webenv' => {
+ 'webenv' => {
'query_key' => 'querykey',
'WebEnv' => 'cookie',
'db' => 'nucleotide',
View
1  Bio/DB/Query/GenBank.pm
@@ -100,6 +100,7 @@ use strict;
use URI::Escape 'uri_unescape';
use Bio::DB::NCBIHelper;
+
#use constant EPOST => $Bio::DB::NCBIHelper::HOSTBASE . '/entrez/eutils/epost.fcgi';
#use constant ESEARCH => $Bio::DB::NCBIHelper::HOSTBASE . '/entrez/eutils/esearch.fcgi';
# the reference to the our variable of the $Bio::DB::NCBIHelper::HOSTBASE doesn't seem to work in
View
26 Bio/DB/WebDBSeqI.pm
@@ -101,9 +101,9 @@ use base qw(Bio::DB::RandomAccessI);
BEGIN {
$MODVERSION = '0.8';
%RETRIEVAL_TYPES = ('io_string' => 1,
- 'tempfile' => 1,
- 'pipeline' => 1,
- );
+ 'tempfile' => 1,
+ 'pipeline' => 1,
+ );
$DEFAULT_RETRIEVAL_TYPE = 'pipeline';
$DEFAULTFORMAT = 'fasta';
$LAST_INVOCATION_TIME = 0;
@@ -449,7 +449,7 @@ sub get_seq_stream {
}
my $request = $self->get_request(%qualifiers);
$request->proxy_authorization_basic($self->authentication)
- if ( $self->authentication);
+ if ( $self->authentication);
$self->debug("request is ". $request->as_string(). "\n");
# workaround for MSWin systems
@@ -467,15 +467,15 @@ sub get_seq_stream {
my ($result,$stream) = $self->_open_pipe();
if (defined $result) {
- $DB::fork_TTY = File::Spec->devnull; # prevents complaints from debugge
+ $DB::fork_TTY = File::Spec->devnull; # prevents complaints from debugger
if (!$result) { # in child process
- $self->_stream_request($request,$stream);
- POSIX::_exit(0); #prevent END blocks from executing in this forked child
+ $self->_stream_request($request,$stream);
+ POSIX::_exit(0); #prevent END blocks from executing in this forked child
}
else {
return Bio::SeqIO->new('-verbose' => $self->verbose,
- '-format' => $ioformat,
- '-fh' => $stream);
+ '-format' => $ioformat,
+ '-fh' => $stream);
}
}
else {
@@ -492,7 +492,7 @@ sub get_seq_stream {
$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( $self->verbose > 0 ) {
@@ -514,11 +514,11 @@ sub get_seq_stream {
}
($rformat,$ioformat) = $self->request_format();
$self->postprocess_data('type'=> 'string',
- 'location' => $content);
+ 'location' => $content);
$self->debug( "str is $$content\n");
return Bio::SeqIO->new('-verbose' => $self->verbose,
- '-format' => $ioformat,
- '-fh' => new IO::String($$content));
+ '-format' => $ioformat,
+ '-fh' => new IO::String($$content));
}
# if we got here, we don't know how to handle the retrieval type
View
13 scripts/utilities/bp_download_query_genbank.pl
@@ -100,9 +100,10 @@ =head1 AUTHOR Jason Stajich
close($fh);
while( @ids ) {
my @mini_ids = splice(@ids, 0, $options{'-maxids'});
- $query = Bio::DB::Query::GenBank->new(%options,
- -ids => \@mini_ids,
- );
+ $query = Bio::DB::Query::GenBank->new(%options,
+ -verbose =>$debug,
+ -ids => \@mini_ids,
+ );
my $stream = $dbh->get_Stream_by_query($query);
while( my $seq = $stream->next_seq ) {
$out->write_seq($seq);
@@ -110,14 +111,14 @@ =head1 AUTHOR Jason Stajich
}
exit;
} elsif( $options{'-query'}) {
- $query = Bio::DB::Query::GenBank->new(%options);
+ $query = Bio::DB::Query::GenBank->new(%options,-verbose => $debug);
} elsif( $queryfile ) {
- open(my $fh => $queryfile) || die "cannot open $queryfile: $!";
+ open(my $fh => $queryfile) || die $!;
while(<$fh>) {
chomp;
$options{'-query'} .= $_;
}
- $query = Bio::DB::Query::GenBank->new(%options);
+ $query = Bio::DB::Query::GenBank->new(%options,-verbose => $debug);
close($fh);
} else {
die("no query string or gifile\n");
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