[med-svn] [bioperl] 04/10: Imported Upstream version 1.7~rc4
Charles Plessy
plessy at moszumanska.debian.org
Mon Jul 11 13:09:18 UTC 2016
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch master
in repository bioperl.
commit baf036722d9c597adfc0802415b841643dbae31c
Author: Charles Plessy <plessy at debian.org>
Date: Mon Jul 11 21:43:07 2016 +0900
Imported Upstream version 1.7~rc4
---
Bio/Root/Version.pm | 2 +-
Bio/Tools/Analysis/Protein/Mitoprot.pm | 327 --------------------------
Build.PL | 7 +-
DEPENDENCIES | 2 -
MANIFEST | 2 -
META.json | 14 +-
META.yml | 13 +-
examples/db/getGenBank.pl | 2 +-
examples/db/get_seqs.pl | 2 +-
examples/generate_random_seq.pl | 2 +-
examples/searchio/psiblast_features.pl | 2 +-
examples/structure/structure-io.pl | 2 +-
examples/tk/hitdisplay.pl | 2 +-
examples/tools/gb_to_gff.pl | 2 +-
maintenance/big_split/file_classification.csv | 4 -
t/Assembly/ContigSpectrum.t | 9 +-
t/LocalDB/Taxonomy/sqlite.t | 40 +---
t/RemoteDB/Taxonomy.t | 1 -
t/Root/IO.t | 24 +-
t/Seq/PrimarySeq.t | 7 +
t/Tools/Analysis/Protein/Mitoprot.t | 37 ---
21 files changed, 56 insertions(+), 447 deletions(-)
diff --git a/Bio/Root/Version.pm b/Bio/Root/Version.pm
index 1346148..93d65fa 100644
--- a/Bio/Root/Version.pm
+++ b/Bio/Root/Version.pm
@@ -36,7 +36,7 @@ variable set if it's not already.
=cut
-our $VERSION = '1.007000_003';
+our $VERSION = '1.007000_004';
sub import {
# try to handle multiple levels of inheritance:
diff --git a/Bio/Tools/Analysis/Protein/Mitoprot.pm b/Bio/Tools/Analysis/Protein/Mitoprot.pm
deleted file mode 100644
index 717191d..0000000
--- a/Bio/Tools/Analysis/Protein/Mitoprot.pm
+++ /dev/null
@@ -1,327 +0,0 @@
-# $Id: Mitoprot.pm,
-#
-# BioPerl module for Bio::Tools::Analysis::Protein::Mitoprot
-# Copyright Richard Adams
-#
-# You may distribute this module under the same terms as perl itself
-# POD documentation - main docs before the code
-
-=head1 NAME
-
-Bio::Tools::Analysis::Protein::Mitoprot - a wrapper around Mitoprot
-server
-
-=head1 SYNOPSIS
-
- use Bio::Tools::Analysis::Protein::Mitoprot;
-
- use Bio::PrimarySeq;
- my $seq = Bio::PrimarySeq->new
- (-seq=>'IKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL',
- -primary_id=>'test'); # a Bio::PrimarySeqI object
-
- my $mitoprot = Bio::Tools::Analysis::Protein::Mitoprot->new
- ( -seq => $seq
- ); # sequence must be >!5aa long and start with an M.
-
- # run Mitoprot prediction on a DNA sequence
- my $mitoprot->run();
-
-
- die "Could not get a result" unless $mitoprot->status =~ /^COMPLETED/;
-
- print $mitoprot->result; # print raw prediction to STDOUT
-
- foreach my $feat ( $mitoprot->result('Bio::SeqFeatureI') ) {
-
- # do something to SeqFeature
- # e.g. print as GFF
- print $feat->gff_string, "\n";
- # or store within the sequence - if it is a Bio::RichSeqI
- $seq->add_SeqFeature($feat);
-
- }
-
-=head1 DESCRIPTION
-
-This class is a wrapper around the Mitoprot web server which
-calculates the probability of a sequence containing a mitochondrial
-targetting peptide. See http://mips.gsf.de/cgi-bin/proj/medgen/mitofilter
-for more details.
-
-The results can be obtained in 3 formats:
-
-=over 3
-
-=item 1
-
-The raw text of the program output
-
- my $rawdata = $analysis_object->result;
-
-=item 2
-
-An reference to a hash of scores :
-
- my $data_ref = $analysis_object->result('parsed'); print "predicted
- export prob is $data_ref->{'export_prob'}\n"; #
-
-key values of returned hash are input_length, basic_aas, acidic_aas,
-export_prob, charge, cleavage_site.
-
-=item 3
-
-A Bio::SeqFeature::Generic object
-
- my $ft = $analysis_object->result(Bio::SeqFeatureI);
- print "export prob is ", ($ft->each_tag_value('export_prob'))[0] ,"\n";
-
-
-This the second implentation of Bio::SimpleAnalysisI which hopefully
-will make it easier to write wrappers on various services. This class
-uses a web resource and therefore inherits from Bio::WebAgent.
-
-=back
-
-=head1 SEE ALSO
-
-L<Bio::SimpleAnalysisI>,
-L<Bio::Tools::Analysis::SimpleAnalysisBase>,
-L<Bio::WebAgent>
-
-=head1 FEEDBACK
-
-=head2 Mailing Lists
-
-User feedback is an integral part of the evolution of this and other
-Bioperl modules. Send your comments and suggestions preferably to one
-of the Bioperl mailing lists. Your participation is much appreciated.
-
- bioperl-l at bioperl.org - General discussion
- http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-
-=head2 Support
-
-Please direct usage questions or support issues to the mailing list:
-
-I<bioperl-l at 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
-with code and data examples if at all possible.
-
-=head2 Reporting Bugs
-
-Report bugs to the Bioperl bug tracking system to help us keep track
-the bugs and their resolution. Bug reports can be submitted via the
-web:
-
- https://github.com/bioperl/bioperl-live/issues
-
-=head1 AUTHORS
-
-Richard Adams, Richard.Adams at ed.ac.uk,
-
-=head1 APPENDIX
-
-The rest of the documentation details each of the object
-methods. Internal methods are usually preceded with a _
-
-=cut
-
-
-# Let the code begin...
-
-
-package Bio::Tools::Analysis::Protein::Mitoprot;
-use vars qw($FLOAT);
-use strict;
-
-use IO::String;
-use Bio::SeqIO;
-use HTTP::Request::Common qw(GET);
-use Bio::SeqFeature::Generic;
-
-use base qw(Bio::Tools::Analysis::SimpleAnalysisBase);
-$FLOAT = '[+-]?\d*\.\d*';
-
-my $URL = 'https://ihg.gsf.de/cgi-bin/paolo/mitofilter?';
-
-my %STATUS = map { $_ => 1 } qw(CREATED COMPLETED TERMINATED_BY_ERROR);
-
-my $MIN_LEN = 60; #min len for protein analysis
-my $ANALYSIS_NAME = "Mitoprot";
-
-my $ANALYSIS_SPEC =
- {
- 'name' => 'Mitoprot',
- 'type' => 'Protein',
- 'version' => '1.0a4',
- 'supplier' => 'Munich Information Center for ProteinSequences',
- 'description' => 'mitochondrial sig seq prediction',
- };
-
-my $INPUT_SPEC =
- [
- {
- 'mandatory' => 'true',
- 'type' => 'Bio::PrimarySeqI',
- 'name' => 'seq', #value must be name of method used to set value
- },
- ];
-
-my $RESULT_SPEC =
- {
- '' => 'raw text results', # same as undef
- 'Bio::SeqFeatureI' => 'ARRAY of Bio::SeqFeature::Generic',
- 'all' => 'hash of results',
- };
-
-
-
-### unique to this module ##
-
-=head2 result
-
- Usage : $job->result (...)
- Returns : a result created by running an analysis
- Args : various
-
-The method returns a result of an executed job. If the job was
-terminated by an error the result may contain an error message instead
-of the real data.
-
-This implementation returns differently processed data depending on
-argument:
-
-=over 3
-
-=item undef
-
-Returns the raw ASCII data stream but without HTML tags
-
-=item 'Bio::SeqFeatureI'
-
-The argument string defines the type of bioperl objects returned in an
-array. The objects are L<Bio::SeqFeature::Generic>. Feature primary
-tag is "SigSeq". Feature tags are input_length , basic_aas,
-acidic_aas, export_prob, charge, cleavage_site, method.
-
-=item 'parsed'
-
-hash references of parsed results { input_length =E<gt>, basic_aas=E<gt>,
-acidic_aas=E<gt>, export_prob=E<gt>, charge=E<gt>, cleavage_site=E<gt>}.
-
-=back
-
-=cut
-
-
-sub result {
- my ($self,$value) = @_;
- #make sec feat of above threshold scores #
-
- my @sig_pdctns;
- my @fts;
-
- if ($value ) {
- my $result = IO::String->new($self->{'_result'});
- my %results;
- while (my $line = <$result>) {
- #make array of all scores or threshold depending on $value
- next unless $line =~ /\d/ || $line =~ /^Cle/;
- if ($line =~ /^Net[^+\-\d]+ # Net, then anything except +,- or digit
- ((\+|-)?\d+)/x) #then get charge with optional + or -
- {
- $results{'charge'} = $1;
- } elsif ($line =~ /^Input[^\d]+(\d+)/ ) {
- $results{'input_length'} = $1;
- } elsif ($line =~ /basic[^\d]+(\d+)$/ ) {
- $results{'basic_aas'} = $1;
- } elsif ($line =~ /acidic[^\d]+(\d+)$/) {
- $results{'acidic_aas'} = $1;
- } elsif ($line =~ /^Cleavage[^\d]+(\d+)$/) {
- $results{'cleavage_site'} = $1;
- } elsif ($line =~ /^Cleavage/) {
- $results{'cleavage_site'} = 'not predictable';
- } elsif ($line =~ /^of export[^\d]+((0|1)\.\d+)$/) {
- $results{'export_prob'} = $1;
- }
- }
-
- if ($value eq 'Bio::SeqFeatureI') {
- push @fts, Bio::SeqFeature::Generic->new
- (
- -start => 1,
- -end => ($results{'cleavage_site'} =~
- /^\d+$/)?$results{'cleavage_site'}:$self->seq->length,
- -source => 'Mitoprot',
- -primary => 'Region',
- -tag =>{
- export_prob => $results{'export_prob'},
- charge => $results{'charge'},
- basic_aas => $results{'basic_aas'},
- acid_aas => $results{'acidic_aas'},
- region_name => 'Transit_peptide',
- method => 'MitoProt',
- cleavage_site => $results{'cleavage_site'},
- },
- );
- return @fts; #return Bioseqfeature array
- }
- ## convert parsed data into a meta array format
- else {
- return \%results; # hash based results ref
- }
- }
- return $self->{'_result'};
-}
-
-sub _init {
- my $self = shift;
- $self->url($URL);
- $self->{'_ANALYSIS_SPEC'} =$ANALYSIS_SPEC;
- $self->{'_INPUT_SPEC'} =$INPUT_SPEC;
- $self->{'_RESULT_SPEC'} =$RESULT_SPEC;
- $self->{'_ANALYSIS_NAME'} =$ANALYSIS_SPEC->{'name'};
- return $self;
-}
-
-sub _process_arguments {
- #extra checking for sequence length
- #mitoprot specific argument testing
- my ($self, $args) = @_;
- #use base checking for existence of mandatory fields
- $self->SUPER::_process_arguments($args) ;
-
- #then check specifics
- $self->throw ("1st_aa must be M") if $self->seq->subseq(1,1) !~ /M/i;
- $self->throw ("sequence must be at least 15aa long") if $self->seq->length< 15;
- return;
-}
-
-
-
-sub _run {
- #request submitted by get not by post
- my $self = shift;
- $self->delay(1);
- $self->sleep;
-
- $self->status('TERMINATED_BY_ERROR');
- my $url = $self->url . "seq=" . lc($self->seq->seq) . "&seqnam=";
- my $request = GET $url;
- my $content = $self->request($request);
- my $text = $content->content; #1st reponse
-
- #remove html stuff
- $text =~ s/.*<PRE>(.*)<\/PRE>.*/$1/s;
- $text =~ s/<[^>]+>//sg;
-
- $self->status('COMPLETED') if $text ne '' && $self->seq->length > $MIN_LEN;
- $self->{'_result'} = $text;
-
-}
-
-1;
diff --git a/Build.PL b/Build.PL
index 8b5007d..af3ce3c 100644
--- a/Build.PL
+++ b/Build.PL
@@ -135,8 +135,6 @@ my %recommends = (
'Set::Scalar' => [ 0, 'Proper operation/Bio::Tree::Compatible' ],
- 'SOAP::Lite' => [ 0, 'Bibliographic queries/Bio::DB::Biblio::soap' ],
-
'Sort::Naturally' => [
0,
'Sort lexically, but sort numeral parts numerically/'
@@ -167,7 +165,7 @@ my %recommends = (
'XML::LibXML' =>
[ 0, 'Parsing XML/Bio::SeqIO::seqxml,Bio::TreeIO::phyloxml' ],
- 'XML::Parser' => [ 0, 'Parsing XML/Bio::Biblio::IO::medlinexml' ],
+ 'XML::Parser' => [ 0, 'Parsing XML/Bio::OntologyIO::InterProParser' ],
'XML::Parser::PerlSAX' => [
0,
@@ -189,8 +187,7 @@ my %recommends = (
'XML::Twig' => [
0,
- 'Parsing XML/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez,'
- . 'Bio::DB::Biblio::eutils'
+ 'Parsing XML/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez'
],
'XML::Writer' => [
diff --git a/DEPENDENCIES b/DEPENDENCIES
index 9b0e39d..a74403f 100644
--- a/DEPENDENCIES
+++ b/DEPENDENCIES
@@ -147,7 +147,6 @@ NB: This list of packages is not authoritative. See the 'requires',
|------------------------------------------------------------------------------|
| * Bio::PhyloNetwork - IO::String |
| * Bio::DB::CUTG - IO::String |
-| * Bio::DB::SeqHound - IO::String |
| * Bio::DB::WebDBSeqI - IO::String |
| * Bio::Index::Blast - IO::String |
| * Bio::Index::BlastTable - IO::String |
@@ -159,7 +158,6 @@ NB: This list of packages is not authoritative. See the 'requires',
| * Bio::Tools::Analysis::Protein::ELM - IO::String |
| * Bio::Tools::Analysis::Protein::GOR4 - IO::String |
| * Bio::Tools::Analysis::Protein::HNN - IO::String |
-| * Bio::Tools::Analysis::Protein::Mitoprot - IO::String |
| * Bio::Tools::Analysis::Protein::NetPhos - IO::String |
| * Bio::Tools::Analysis::Protein::Scansite - IO::String |
| * Bio::Tools::Analysis::Protein::Sopma - IO::String |
diff --git a/MANIFEST b/MANIFEST
index 7b747bc..ff2facd 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -668,7 +668,6 @@ Bio/Tools/Analysis/Protein/Domcut.pm
Bio/Tools/Analysis/Protein/ELM.pm
Bio/Tools/Analysis/Protein/GOR4.pm
Bio/Tools/Analysis/Protein/HNN.pm
-Bio/Tools/Analysis/Protein/Mitoprot.pm
Bio/Tools/Analysis/Protein/NetPhos.pm
Bio/Tools/Analysis/Protein/Scansite.pm
Bio/Tools/Analysis/Protein/Sopma.pm
@@ -2024,7 +2023,6 @@ t/Tools/Analysis/Protein/Domcut.t
t/Tools/Analysis/Protein/ELM.t
t/Tools/Analysis/Protein/GOR4.t
t/Tools/Analysis/Protein/HNN.t
-t/Tools/Analysis/Protein/Mitoprot.t
t/Tools/Analysis/Protein/NetPhos.t
t/Tools/Analysis/Protein/Scansite.t
t/Tools/Analysis/Protein/Sopma.t
diff --git a/META.json b/META.json
index b9fa154..31b3754 100644
--- a/META.json
+++ b/META.json
@@ -50,7 +50,6 @@
"LWP::UserAgent" : "0",
"List::MoreUtils" : "0",
"PostScript::TextBlock" : "0",
- "SOAP::Lite" : "0",
"SVG" : "2.26",
"SVG::Graph" : "0.01",
"Set::Scalar" : "0",
@@ -231,7 +230,7 @@
"file" : "Bio/Annotation/TypeManager.pm"
},
"Bio::AnnotationCollectionI" : {
- "file" : "Bio/DB/HIV/HIVQueryHelper.pm"
+ "file" : "Bio/AnnotationCollectionI.pm"
},
"Bio::AnnotationI" : {
"file" : "Bio/AnnotationI.pm"
@@ -871,7 +870,7 @@
"file" : "Bio/LiveSeq/Translation.pm"
},
"Bio::LocatableSeq" : {
- "file" : "Bio/Search/Tiling/MapTileUtils.pm"
+ "file" : "Bio/LocatableSeq.pm"
},
"Bio::Location::Atomic" : {
"file" : "Bio/Location/Atomic.pm"
@@ -1364,7 +1363,7 @@
},
"Bio::Root::Build" : {
"file" : "Bio/Root/Build.pm",
- "version" : "1.007000_003"
+ "version" : "1.007000_004"
},
"Bio::Root::Exception" : {
"file" : "Bio/Root/Exception.pm"
@@ -1395,7 +1394,7 @@
},
"Bio::Root::Version" : {
"file" : "Bio/Root/Version.pm",
- "version" : "1.007000_003"
+ "version" : "1.007000_004"
},
"Bio::Search::BlastStatistics" : {
"file" : "Bio/Search/BlastStatistics.pm"
@@ -2111,9 +2110,6 @@
"Bio::Tools::Analysis::Protein::HNN" : {
"file" : "Bio/Tools/Analysis/Protein/HNN.pm"
},
- "Bio::Tools::Analysis::Protein::Mitoprot" : {
- "file" : "Bio/Tools/Analysis/Protein/Mitoprot.pm"
- },
"Bio::Tools::Analysis::Protein::NetPhos" : {
"file" : "Bio/Tools/Analysis/Protein/NetPhos.pm"
},
@@ -2511,5 +2507,5 @@
"http://dev.perl.org/licenses/"
]
},
- "version" : "1.007000_003"
+ "version" : "1.007000_004"
}
diff --git a/META.yml b/META.yml
index 958c43c..deb8505 100644
--- a/META.yml
+++ b/META.yml
@@ -119,7 +119,7 @@ provides:
Bio::Annotation::TypeManager:
file: Bio/Annotation/TypeManager.pm
Bio::AnnotationCollectionI:
- file: Bio/DB/HIV/HIVQueryHelper.pm
+ file: Bio/AnnotationCollectionI.pm
Bio::AnnotationI:
file: Bio/AnnotationI.pm
Bio::Assembly::Contig:
@@ -546,7 +546,7 @@ provides:
Bio::LiveSeq::Translation:
file: Bio/LiveSeq/Translation.pm
Bio::LocatableSeq:
- file: Bio/Search/Tiling/MapTileUtils.pm
+ file: Bio/LocatableSeq.pm
Bio::Location::Atomic:
file: Bio/Location/Atomic.pm
Bio::Location::AvWithinCoordPolicy:
@@ -875,7 +875,7 @@ provides:
file: Bio/Restriction/IO/withrefm.pm
Bio::Root::Build:
file: Bio/Root/Build.pm
- version: 1.007000_003
+ version: 1.007000_004
Bio::Root::Exception:
file: Bio/Root/Exception.pm
Bio::Root::HTTPget:
@@ -896,7 +896,7 @@ provides:
file: Bio/Root/Utilities.pm
Bio::Root::Version:
file: Bio/Root/Version.pm
- version: 1.007000_003
+ version: 1.007000_004
Bio::Search::BlastStatistics:
file: Bio/Search/BlastStatistics.pm
Bio::Search::BlastUtils:
@@ -1373,8 +1373,6 @@ provides:
file: Bio/Tools/Analysis/Protein/GOR4.pm
Bio::Tools::Analysis::Protein::HNN:
file: Bio/Tools/Analysis/Protein/HNN.pm
- Bio::Tools::Analysis::Protein::Mitoprot:
- file: Bio/Tools/Analysis/Protein/Mitoprot.pm
Bio::Tools::Analysis::Protein::NetPhos:
file: Bio/Tools/Analysis/Protein/NetPhos.pm
Bio::Tools::Analysis::Protein::Scansite:
@@ -1656,7 +1654,6 @@ recommends:
LWP::UserAgent: '0'
List::MoreUtils: '0'
PostScript::TextBlock: '0'
- SOAP::Lite: '0'
SVG: '2.26'
SVG::Graph: '0.01'
Set::Scalar: '0'
@@ -1683,4 +1680,4 @@ requires:
perl: v5.6.1
resources:
license: http://dev.perl.org/licenses/
-version: 1.007000_003
+version: 1.007000_004
diff --git a/examples/db/getGenBank.pl b/examples/db/getGenBank.pl
index 01ea6b7..b2621d4 100755
--- a/examples/db/getGenBank.pl
+++ b/examples/db/getGenBank.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
#
# How to retrieve GenBank entries over the Web
#
diff --git a/examples/db/get_seqs.pl b/examples/db/get_seqs.pl
index cf2df29..29c1cf6 100755
--- a/examples/db/get_seqs.pl
+++ b/examples/db/get_seqs.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
use strict;
use vars qw($USAGE);
use Carp;
diff --git a/examples/generate_random_seq.pl b/examples/generate_random_seq.pl
index 2849fac..9eb44bf 100755
--- a/examples/generate_random_seq.pl
+++ b/examples/generate_random_seq.pl
@@ -1,4 +1,4 @@
-#!/bin/perl
+#!/usr/bin/perl
use strict;
use vars qw($USAGE);
diff --git a/examples/searchio/psiblast_features.pl b/examples/searchio/psiblast_features.pl
index e6fbf0c..e98a362 100755
--- a/examples/searchio/psiblast_features.pl
+++ b/examples/searchio/psiblast_features.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
# Example usage of a SearchIO::psiblast parser of traditional format Blast
# and PSI-Blast reports.
diff --git a/examples/structure/structure-io.pl b/examples/structure/structure-io.pl
index 8cec9b4..37d6fee 100755
--- a/examples/structure/structure-io.pl
+++ b/examples/structure/structure-io.pl
@@ -1,4 +1,4 @@
-#!/bin/perl
+#!/usr/bin/perl
# Getting Entry, Chain, Residue, and Atom objects given a PDB file
use Bio::Structure::IO;
diff --git a/examples/tk/hitdisplay.pl b/examples/tk/hitdisplay.pl
index 97a41ad..e808a58 100755
--- a/examples/tk/hitdisplay.pl
+++ b/examples/tk/hitdisplay.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
#
# PROGRAM : hitdisplay.pl
# PURPOSE : Demonstrate Bio::Tk::HitDisplay
diff --git a/examples/tools/gb_to_gff.pl b/examples/tools/gb_to_gff.pl
index bacf12a..eee2ec0 100755
--- a/examples/tools/gb_to_gff.pl
+++ b/examples/tools/gb_to_gff.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
use strict;
use Bio::Tools::GFF;
diff --git a/maintenance/big_split/file_classification.csv b/maintenance/big_split/file_classification.csv
index 03bd4bb..e46fe2b 100644
--- a/maintenance/big_split/file_classification.csv
+++ b/maintenance/big_split/file_classification.csv
@@ -526,7 +526,6 @@
"Bio-DB-SeqFeature","Bio/DB/SeqFeature/NormalizedTableFeatureI.pm"
"AcePerl","Bio/DB/Ace.pm"
,"Bio/DB/GenPept.pm"
-,"Bio/DB/SeqHound.pm"
,"Bio/DB/Flat/BDB.pm"
,"Bio/DB/Flat/BinarySearch.pm"
,"Bio/DB/Flat/BDB/swiss.pm"
@@ -833,7 +832,6 @@
,"Bio/Tools/Analysis/SimpleAnalysisBase.pm"
,"Bio/Tools/Analysis/DNA/ESEfinder.pm"
,"Bio/Tools/Analysis/Protein/Domcut.pm"
-,"Bio/Tools/Analysis/Protein/Mitoprot.pm"
,"Bio/Tools/Analysis/Protein/Sopma.pm"
,"Bio/Tools/Analysis/Protein/NetPhos.pm"
,"Bio/Tools/Analysis/Protein/Scansite.pm"
@@ -2060,7 +2058,6 @@
,"t/RemoteDB/EUtilities.t"
,"t/RemoteDB/EntrezGene.t"
,"t/RemoteDB/BioFetch.t"
-,"t/RemoteDB/SeqHound.t"
,"t/RemoteDB/CUTG.t"
,"t/RemoteDB/Query/GenBank.t"
,"t/RemoteDB/SeqVersion.t"
@@ -2161,7 +2158,6 @@
,"t/Tools/EUtilities/egquery.t"
,"t/Tools/Analysis/DNA/ESEfinder.t"
,"t/Tools/Analysis/Protein/Sopma.t"
-,"t/Tools/Analysis/Protein/Mitoprot.t"
,"t/Tools/Analysis/Protein/GOR4.t"
,"t/Tools/Analysis/Protein/Scansite.t"
,"t/Tools/Analysis/Protein/ELM.t"
diff --git a/t/Assembly/ContigSpectrum.t b/t/Assembly/ContigSpectrum.t
index 760e058..910d441 100644
--- a/t/Assembly/ContigSpectrum.t
+++ b/t/Assembly/ContigSpectrum.t
@@ -313,9 +313,12 @@ SKIP: {
float_is $large_csp->avg_seq_len, 100;
is $large_csp->nof_overlaps, 26;
is $large_csp->min_overlap, 54;
- # operation returns sometimes 88.76923... and sometimes 88.80769...
- ok $large_csp->avg_overlap >= 88.7692;
- ok $large_csp->avg_overlap <= 88.8077;
+
+ # Stochastic test results:
+ # Operation returns sometimes 88.76923... and sometimes 88.80769...
+
+ cmp_ok($large_csp->avg_overlap, '>=', 85);
+ cmp_ok($large_csp->avg_overlap, '<=', 95);
float_is $large_csp->min_identity, 33.3333;
cmp_ok($large_csp->avg_identity, '>=', 70, $large_csp->avg_identity);
cmp_ok($large_csp->avg_identity, '<=', 80, $large_csp->avg_identity);
diff --git a/t/LocalDB/Taxonomy/sqlite.t b/t/LocalDB/Taxonomy/sqlite.t
index 30d8226..ca02db2 100644
--- a/t/LocalDB/Taxonomy/sqlite.t
+++ b/t/LocalDB/Taxonomy/sqlite.t
@@ -7,10 +7,9 @@ BEGIN {
use lib '.';
use Bio::Root::Test;
- #test_begin(
- #
- # -requires_modules => [qw(DBI DBD::SQLite )]
- #);
+ test_begin(
+ -requires_modules => [qw(DB_File DBI DBD::SQLite )]
+ );
use_ok('Bio::DB::Taxonomy');
use_ok('Bio::Tree::Tree');
@@ -29,39 +28,6 @@ ok my $db_flatfile = Bio::DB::Taxonomy->new(
isa_ok $db_flatfile, 'Bio::DB::Taxonomy::sqlite';
isa_ok $db_flatfile, 'Bio::DB::Taxonomy';
-# By not specifying a '-directory' argument, index files go to a temporary
-# folder ($Bio::Root::IO::TEMPDIR, such as 'C:\Users\USER\AppData\Local\Temp'),
-# and are implied to be temporary. So test the ability of flatfile->DESTROY to
-# remove the temporary index files at object destruction (this also affects files
-# in "test_output_dir()", since the folder is created inside the temporary folder)
-#no warnings qw(once); # silence 'Name "$Bio::Root::IO::TEMPDIR" used only once'
-#
-#is $db_flatfile->{index_directory}, $Bio::Root::IO::TEMPDIR, 'removal of temporary index files: no -directory';
-
-#$db_flatfile->DESTROY;
-#ok not -e ($db_flatfile->{index_directory} . '/id2names');
-#ok not -e ($db_flatfile->{index_directory} . '/names2id');
-#ok not -e ($db_flatfile->{index_directory} . '/nodes');
-#ok not -e ($db_flatfile->{index_directory} . '/parents');
-
-## Test removal of temporary index files from test_output_dir folder
-## (since test_output_dir() =~ m/^$Bio::Root::IO::TEMPDIR/)
-#ok $db_flatfile = Bio::DB::Taxonomy->new(
-# -source => 'flatfile',
-# -directory => $temp_dir,
-# -nodesfile => test_input_file('taxdump', 'nodes.dmp'),
-# -namesfile => test_input_file('taxdump', 'names.dmp'),
-# -force => 1,
-#);
-#is $db_flatfile->{index_directory}, $temp_dir, 'removal of temporary index files: test_output_dir()';
-#$db_flatfile->DESTROY;
-#ok not -e ($db_flatfile->{index_directory} . '/id2names');
-#ok not -e ($db_flatfile->{index_directory} . '/names2id');
-#ok not -e ($db_flatfile->{index_directory} . '/nodes');
-#ok not -e ($db_flatfile->{index_directory} . '/parents');
-#
-# Generate the object (and the files) again for the remaining tests
-
ok my $db = Bio::DB::Taxonomy->new(
-source => 'sqlite',
-directory => $temp_dir,
diff --git a/t/RemoteDB/Taxonomy.t b/t/RemoteDB/Taxonomy.t
index bf58bff..f7b5951 100644
--- a/t/RemoteDB/Taxonomy.t
+++ b/t/RemoteDB/Taxonomy.t
@@ -182,7 +182,6 @@ for my $db ($db_entrez, $db_flatfile) {
} else {
# note the locally cached flatfile is out-of-date, but technically
# correct for testing purposes
- diag(join(",", @ids));
ok grep { $_ == 266791 } @ids;
ok grep { $_ == 5533 } @ids;
}
diff --git a/t/Root/IO.t b/t/Root/IO.t
index 23dfe4f..4e95caa 100644
--- a/t/Root/IO.t
+++ b/t/Root/IO.t
@@ -284,22 +284,38 @@ SKIP: {
$expected = "DEFINITION Desmognathus quadramaculatus 12S ribosomal RNA gene, partial\n";
is $unix_rio->_readline, $expected;
- is $win_rio->_readline , $expected;
+ TODO: {
+ local $TODO = "Sporadic test failures when running using PerlIO::eol on Linux w/".
+ "Windows line endings: #";
+ is $win_rio->_readline , $expected;
+ };
is $mac_rio->_readline , $expected;
$expected = " sequence; tRNA-Val gene, complete sequence; and 16S ribosomal RNA\n";
is $unix_rio->_readline, $expected;
- is $win_rio->_readline , $expected;
+ TODO: {
+ local $TODO = "Sporadic test failures when running using PerlIO::eol on Linux w/".
+ "Windows line endings: #";
+ is $win_rio->_readline , $expected;
+ };
is $mac_rio->_readline , $expected;
$expected = " gene, partial sequence, mitochondrial genes for mitochondrial RNAs.\n";
is $unix_rio->_readline, $expected;
- is $win_rio->_readline , $expected;
+ TODO: {
+ local $TODO = "Sporadic test failures when running using PerlIO::eol on Linux w/".
+ "Windows line endings: #";
+ is $win_rio->_readline , $expected;
+ };
is $mac_rio->_readline , $expected;
$expected = "ACCESSION U71225\n";
is $unix_rio->_readline, $expected;
- is $win_rio->_readline , $expected;
+ TODO: {
+ local $TODO = "Sporadic test failures when running using PerlIO::eol on Linux w/".
+ "Windows line endings: #";
+ is $win_rio->_readline , $expected;
+ };
is $mac_rio->_readline , $expected;
# $HAS_EOL ignores -raw
diff --git a/t/Seq/PrimarySeq.t b/t/Seq/PrimarySeq.t
index 93d430e..22fed4a 100644
--- a/t/Seq/PrimarySeq.t
+++ b/t/Seq/PrimarySeq.t
@@ -291,14 +291,21 @@ is $seq->seq('TTGGTGGCG?CAACT'), 'TTGGTGGCG?CAACT';
# frame 1, frame 0 start < frame 1 start, then should return the frame
# 0 ORF per the pod ('the first orf') even if frame 1 stop < frame 0 stop
+# Turn off warnings for a few tests
+my $verbosity = $seq->verbose();
+$seq->verbose(-1);
+
$seq->seq('ATGAATGTAAATAA');
$aa = $seq->translate( -orf => 1 );
my $aa0 = $seq->translate(-frame => 0);
+
is $aa->seq, $aa0->seq, "frame 0 start, frame 1 stop < frame 0 stop";
$seq->seq('AAATGAATGTAAATAA');
$aa = $seq->translate( -orf => 1, -frame=>1 );
my $aa2 = $seq->translate(-frame => 2);
is $aa->seq, $aa2->seq, "frame 1 start, frame 2 stop < frame 1 stop";
+# Turn 'em back on!
+$seq->verbose($verbosity);
# test for some aliases
$seq = Bio::PrimarySeq->new(
diff --git a/t/Tools/Analysis/Protein/Mitoprot.t b/t/Tools/Analysis/Protein/Mitoprot.t
deleted file mode 100644
index 5fe60e8..0000000
--- a/t/Tools/Analysis/Protein/Mitoprot.t
+++ /dev/null
@@ -1,37 +0,0 @@
-# -*-Perl-*- Test Harness script for Bioperl
-# $Id$
-
-use strict;
-
-BEGIN {
- use lib '.';
- use Bio::Root::Test;
-
- test_begin(-tests => 10,
- -requires_modules => [qw(IO::String LWP::UserAgent)],
- -requires_networking => 1);
-
- use_ok 'Bio::Tools::Analysis::Protein::Mitoprot';
- use_ok 'Bio::PrimarySeq';
- use_ok 'Bio::WebAgent';
-}
-
-my $verbose = test_debug();
-
-ok my $tool = Bio::WebAgent->new(-verbose =>$verbose);
-
-my $seq = Bio::PrimarySeq->new(-seq => 'MSADQRWRQDSQDSFGDSFDGDSFFGSDFDGDS'
- . 'DFGSDFGSDGDFGSDFGDSFGDGFSDRSRQDQRS',
- -display_id => 'test2');
-
-ok $tool = Bio::Tools::Analysis::Protein::Mitoprot->new( -seq=>$seq);
-SKIP: {
- ok $tool->run();
- skip( 'Server terminated with an error, skipping tests', 4 )
- if ( $tool->status eq 'TERMINATED_BY_ERROR'
- or $tool->result =~ /Can't connect to/ );
- ok my $raw = $tool->result('');
- ok my $parsed = $tool->result('parsed');
- is ($parsed->{'charge'}, -13);
- ok my @res = $tool->result('Bio::SeqFeatureI');
-}
--
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