Commit e915263d authored by Andreas Tille's avatar Andreas Tille

New upstream version 1.5.2

parent 35cfab6c
commit 68f87dc3c4488155992f88c3cf1db27061948315
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Sep 20 13:25:35 2018 +0900
add changes made for bioruby-1.5.2
RELEASE_NOTES.rdoc | 14 ++++++++++++++
1 file changed, 14 insertions(+)
commit 6b7e87abfbab88a3bb1b80227ab4b0cfaaeae26e
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Sep 20 13:24:45 2018 +0900
regenerate bioruby.gemspec with rake regemspec
bioruby.gemspec | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
commit a7dbefeef20d6dea18f0bdd67df24e00c5e9ede6
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Sep 20 13:23:31 2018 +0900
version changed to 1.5.2
lib/bio/version.rb | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
commit e00134a1a31db46421b6d468ea1c1d0368bfbb6c
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Sep 20 12:55:32 2018 +0900
Bug fix: printf format syntax error about single percent character
* Bio::Shell#seqstat: Fix format specifier syntax error.
Recent version of Ruby raised error: 'ArgumentError:
incomplete format specifier;use %% (double %) instead'.
lib/bio/shell/plugin/seq.rb | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
commit df61cdba5ba3e90fda6c70cc9f880567656a5a82
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Sep 20 07:06:08 2018 +0900
Improvement documentation
* Improve documentation.
* Close https://github.com/bioruby/bioruby/pull/120 .
lib/bio/db/aaindex.rb | 79 +++++++++++++++++++++++++++++++++++++++++++++++----
1 file changed, 74 insertions(+), 5 deletions(-)
commit 35bcc5008c7721afb3c16467ae6dc782651f4c39
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Sep 20 05:01:12 2018 +0900
Bug fix: Bio::Command.new_https should support proxy
lib/bio/command.rb | 18 +++++++-----------
1 file changed, 7 insertions(+), 11 deletions(-)
commit 88b58e94d4612f39abb14b89779ceeb533cd552e
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Sep 20 04:58:56 2018 +0900
https support for Bio::Blast::Remote::GenomeNet::Information
lib/bio/appl/blast/genomenet.rb | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
commit dfccbdf32bf819f941f2bcb4f63b2f0ce12cacfa
Author: ramadis <rramiro.o@hotmail.com>
Date: Sat Jul 7 15:12:33 2018 -0300
Add https requests in command. Fix genomenet query by allowing https requests.
lib/bio/appl/blast/genomenet.rb | 2 +-
lib/bio/command.rb | 14 ++++++++++++++
2 files changed, 15 insertions(+), 1 deletion(-)
commit d1e1358c1a5c7c7f4aa093a09d5bb45b60f7e7ee
Author: markwilkinson <markw@illuminae.com>
Date: Tue Dec 12 14:13:51 2017 +0100
fixing Fasta Report parser for fasta36 -m10
lib/bio/appl/fasta/format10.rb | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
commit b9b11f66733e20e1ee6d2b5e0aab813b5b5d0000
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Sep 13 22:13:59 2017 +0900
Suppress warning "assigned but unused variable"
lib/bio/io/flatfile/autodetection.rb | 5 +++++
1 file changed, 5 insertions(+)
commit 580dd6bb9344c2afd0fe60b0cf53a4b28734fbbf
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Sep 13 22:10:53 2017 +0900
Suppress warning: "instance variable @top_strand not initialized"
* Suppress warning: "instance variable @top_strand not initialized".
To do so, force to raise NoMethodError when @top_strand is not
initialized or is nil. This should be changed to appropriate
exception in the future.
lib/bio/util/sirna.rb | 2 ++
1 file changed, 2 insertions(+)
commit 9d7ef4e66ecdc1aadc08fda4b332a51ca7739c82
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Sep 13 21:31:38 2017 +0900
Suppress warning in Ruby 2.4: "constant ::Fixnum is deprecated"
lib/bio/db/soft.rb | 4 ++--
.../util/restriction_enzyme/range/sequence_range/calculated_cuts.rb | 2 +-
test/unit/bio/test_alignment.rb | 4 ++--
3 files changed, 5 insertions(+), 5 deletions(-)
commit 2747ee11392068de88e044abf52d12a88a0624ea
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Sep 13 21:19:12 2017 +0900
Suppress warning "parentheses after method name is interpreted as an argument list, not a decomposed argument" in Ruby 2.4
lib/bio/map.rb | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
commit 1edbd88a703d3cff0f5a29e45fa51058405ab58c
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Sep 7 22:06:32 2016 +0900
BioRuby 1.5.1 is released
ChangeLog | 690 +++++++++++++++++++++++++++++++++++---------------------------
1 file changed, 385 insertions(+), 305 deletions(-)
commit 917fe0d0e9910267cd54bf48c2caabe89875a299
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Sep 7 22:00:56 2016 +0900
......@@ -1916,11 +2057,9 @@ Date: Fri Jun 28 15:26:20 2013 +0900
rename test/unit/bio/db/embl/test_uniprot_new_part.rb to test_uniprotkb_new_part.rb
test/unit/bio/db/embl/test_uniprot_new_part.rb | 208 -----------------------
test/unit/bio/db/embl/test_uniprotkb_new_part.rb | 208 +++++++++++++++++++++++
2 files changed, 208 insertions(+), 208 deletions(-)
delete mode 100644 test/unit/bio/db/embl/test_uniprot_new_part.rb
create mode 100644 test/unit/bio/db/embl/test_uniprotkb_new_part.rb
.../bio/db/embl/{test_uniprot_new_part.rb => test_uniprotkb_new_part.rb} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
rename test/unit/bio/db/embl/{test_uniprot_new_part.rb => test_uniprotkb_new_part.rb} (100%)
commit 1b51d0940712a6f144f8268dc77048bc7ec7d983
Author: Naohisa Goto <ng@bioruby.org>
......@@ -1940,11 +2079,9 @@ Date: Fri Jun 28 15:01:15 2013 +0900
test_sptr.rb is renamed to test_uniprotkb.rb
test/unit/bio/db/embl/test_sptr.rb | 1807 -------------------------------
test/unit/bio/db/embl/test_uniprotkb.rb | 1807 +++++++++++++++++++++++++++++++
2 files changed, 1807 insertions(+), 1807 deletions(-)
delete mode 100644 test/unit/bio/db/embl/test_sptr.rb
create mode 100644 test/unit/bio/db/embl/test_uniprotkb.rb
test/unit/bio/db/embl/{test_sptr.rb => test_uniprotkb.rb} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
rename test/unit/bio/db/embl/{test_sptr.rb => test_uniprotkb.rb} (100%)
commit e1ed7fab4c0350e6866dd420a93e950c53063f38
Author: Naohisa Goto <ng@bioruby.org>
......@@ -1998,11 +2135,9 @@ Date: Thu Jun 27 18:16:38 2013 +0900
Rename lib/bio/db/embl/sptr.rb to uniprotkb.rb
lib/bio/db/embl/sptr.rb | 1456 ------------------------------------------
lib/bio/db/embl/uniprotkb.rb | 1456 ++++++++++++++++++++++++++++++++++++++++++
2 files changed, 1456 insertions(+), 1456 deletions(-)
delete mode 100644 lib/bio/db/embl/sptr.rb
create mode 100644 lib/bio/db/embl/uniprotkb.rb
lib/bio/db/embl/{sptr.rb => uniprotkb.rb} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
rename lib/bio/db/embl/{sptr.rb => uniprotkb.rb} (100%)
commit 2a10ded8e1502e0db5ec3b2e060f658ee53aafd0
Author: Naohisa Goto <ng@bioruby.org>
......@@ -2951,11 +3086,9 @@ Date: Thu Aug 23 00:20:01 2012 +0900
renamed ChangeLog to doc/ChangeLog-1.4.3
ChangeLog | 1478 ---------------------------------------------------
doc/ChangeLog-1.4.3 | 1478 +++++++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 1478 insertions(+), 1478 deletions(-)
delete mode 100644 ChangeLog
create mode 100644 doc/ChangeLog-1.4.3
ChangeLog => doc/ChangeLog-1.4.3 | 0
1 file changed, 0 insertions(+), 0 deletions(-)
rename ChangeLog => doc/ChangeLog-1.4.3 (100%)
commit 0c20cb62ba6b253098e7198c14de1829f72474f5
Author: Naohisa Goto <ng@bioruby.org>
......@@ -2982,11 +3115,9 @@ Date: Thu Aug 23 00:12:40 2012 +0900
Renamed RELEASE_NOTES.rdoc to doc/RELEASE_NOTES-1.4.3.rdoc
RELEASE_NOTES.rdoc | 204 -------------------------------------------
doc/RELEASE_NOTES-1.4.3.rdoc | 204 +++++++++++++++++++++++++++++++++++++++++++
2 files changed, 204 insertions(+), 204 deletions(-)
delete mode 100644 RELEASE_NOTES.rdoc
create mode 100644 doc/RELEASE_NOTES-1.4.3.rdoc
RELEASE_NOTES.rdoc => doc/RELEASE_NOTES-1.4.3.rdoc | 0
1 file changed, 0 insertions(+), 0 deletions(-)
rename RELEASE_NOTES.rdoc => doc/RELEASE_NOTES-1.4.3.rdoc (100%)
commit 08bcabecccb271385d38a0f807e8c408def5a128
Author: Naohisa Goto <ng@bioruby.org>
......
= BioRuby 1.5.2 RELEASE NOTES
Few bug fixes have been made to the BioRuby 1.5.2 after the version 1.5.1 is
released.
* Fixed a parser bug in Bio::Fasta::Report, FASTA output (-m 10) parser,
contributed by William Van Etten and Mark Wilkinson via GitHub.
* HTTPS is used to access GenomeNet BLAST web service, contributed
by @ramadis via GitHub.
* Bio::Shell#seqstat: Fix format specifier syntax error.
* Bio::AAindex documentation fix, suggested by @kojix2 via GitHub.
* Suppress warning messages in Ruby 2.4 and later.
= BioRuby 1.5.1 RELEASE NOTES
Few changes have been made to the BioRuby 1.5.1 after the version 1.5.0 is
......
......@@ -3,7 +3,7 @@
#
Gem::Specification.new do |s|
s.name = 'bio'
s.version = "1.5.1"
s.version = "1.5.2"
s.author = "BioRuby project"
s.email = "staff@bioruby.org"
......
......@@ -102,7 +102,7 @@ module Bio::Blast::Remote
dbdescs = {}
key = nil
host = Bio::Blast::Remote::Genomenet::Host
http = Bio::Command.new_http(host)
http = Bio::Command.new_https(host)
result = http.get('/tools/blast/')
#p result.body
result.body.each_line do |line|
......@@ -211,7 +211,7 @@ module Bio::Blast::Remote
end
begin
http = Bio::Command.new_http(host)
http = Bio::Command.new_https(host)
http.open_timeout = 300
http.read_timeout = 600
result = Bio::Command.http_post_form(http, path, form)
......@@ -243,10 +243,10 @@ module Bio::Blast::Remote
end
# workaround 2005.08.12 + 2011.01.27 + 2011.7.22
if /\<A +HREF=\"(http\:\/\/[\-\.a-z0-9]+\.genome\.jp)?(\/tmp\/[^\"]+)\"\>Show all result\<\/A\>/i =~ @output.to_s then
if /\<A +HREF=\"(https?\:\/\/[\-\.a-z0-9]+\.genome\.jp)?(\/tmp\/[^\"]+)\"\>Show all result\<\/A\>/i =~ @output.to_s then
all_prefix = $1
all_path = $2
all_prefix = "http://#{Host}" if all_prefix.to_s.empty?
all_prefix = "https://#{Host}" if all_prefix.to_s.empty?
all_uri = all_prefix + all_path
@output = Bio::Command.read_uri(all_uri)
case all_path
......
......@@ -94,8 +94,9 @@ class Report
# header lines - brief list of the hits
if list_start = data.index("\nThe best scores are") then
data = data[(list_start + 1)..-1]
data.sub!(/(.*)\n\n>>>/m, '')
data.sub!(/(.*?)\n\n>>>/m, '')
@list = $1
data.sub!(/>>><<<(.*)$/m, '')
else
if list_start = data.index(/\n!!\s+/) then
data = data[list_start..-1]
......
......@@ -791,6 +791,16 @@ module Command
end
end
# Same as:
# h = Bio::Command.new_http(address, port)
# h.use_ssl = true
# h
def new_https(address, port = 443)
connection = new_http(address, port)
connection.use_ssl = true
connection
end
# Same as:
# http = Net::HTTP.new(...); http.post_form(path, params)
# and
......
......@@ -7,12 +7,11 @@
# Mitsuteru C. Nakao <n@bioruby.org>
# License:: The Ruby License
#
# $Id:$
#
# == Description
#
# Classes for Amino Acid Index Database (AAindex and AAindex2).
# * AAindex Manual: http://www.genome.jp/dbget-bin/show_man?aaindex
# * AAindex Help: https://www.genome.jp/aaindex/aaindex_help.html
#
# == Examples
#
......@@ -40,7 +39,38 @@ require "matrix"
module Bio
# Super class for AAindex1 and AAindex2
# == Description
#
# Bio::AAindex is the super class of Bio::AAindex1 and Bio::AAindex2,
# parser classes for AAindex Amino Acid Index Database.
# * AAindex Help: https://www.genome.jp/aaindex/aaindex_help.html
#
# Except Bio::AAindex.auto, do not use this class directly.
# Methods of this super class is used from AAindex1 and AAindex2 classes.
#
# == Examples
#
# # auto-detection of data format
# aax1 = Bio::AAindex.auto("PRAM900102.aaindex1")
# aax2 = Bio::AAindex.auto("DAYM780301.aaindex2")
#
# # Example of Bio::AAindex1 class
# aax1 = Bio::AAindex1.new("PRAM900102.aaindex1")
# aax1.entry_id
# aax1.index
#
# # Example of Bio::AAindex2 class
# aax2 = Bio::AAindex2.new("DAYM780301.aaindex2")
# aax2.entry_id
# aax2.matrix
# aax2.matrix[2,2]
# aax2.matrix('R', 'A')
# aax2['R', 'A']
#
# == References
#
# * http://www.genome.jp/aaindex/
#
class AAindex < KEGGDB
# Delimiter
......@@ -136,7 +166,25 @@ module Bio
end
# Class for AAindex1 format.
# == Description
#
# Parser class for AAindex1, Amino Acid Index Database.
# * AAindex Help: https://www.genome.jp/aaindex/aaindex_help.html
#
# == Examples
#
# # auto-detection of data format by using Bio::AAindex class
# aax1 = Bio::AAindex.auto("PRAM900102.aaindex1")
#
# # parse a file and get contents
# aax1 = Bio::AAindex1.new("PRAM900102.aaindex1")
# aax1.entry_id
# aax1.index
#
# == References
#
# * http://www.genome.jp/aaindex/
#
class AAindex1 < AAindex
def initialize(entry)
......@@ -211,7 +259,28 @@ module Bio
end
# Class for AAindex2 format.
# == Description
#
# Parser class for AAindex2, Amino Acid Index Database.
# * AAindex Help: https://www.genome.jp/aaindex/aaindex_help.html
#
# == Examples
#
# # auto-detection of data format by using Bio::AAindex class
# aax2 = Bio::AAindex.auto("DAYM780301.aaindex2")
#
# # parse a file and get contents
# aax2 = Bio::AAindex2.new("DAYM780301.aaindex2")
# aax2.entry_id
# aax2.matrix
# aax2.matrix[2,2]
# aax2.matrix('R', 'A')
# aax2['R', 'A']
#
# == References
#
# * http://www.genome.jp/aaindex/
#
class AAindex2 < AAindex
def initialize(entry)
......
......@@ -217,13 +217,13 @@ class SOFT
end
def [](x)
if x.kind_of?( Fixnum )
if x.kind_of?( Integer )
super(x)
else
begin
x = x.to_s.downcase.to_sym
z = @header_object.column_index[x]
unless z.kind_of?( Fixnum )
unless z.kind_of?( Integer )
raise IndexError, "#{x.inspect} is not a valid index. Contents of @header_object.column_index: #{@header_object.column_index.inspect}"
end
self[ z ]
......
......@@ -547,6 +547,11 @@ module Bio
#BottomRule.is_prior_to(debug_last)
#fastaformat.is_prior_to(debug_last)
## for suppressing warnings
p medline, aaindex, litdb, fantom, clustal,
gcg_msf, gcg_seq, blastxml, rpsblast, blat,
spidey, hmmer, sim4 if false
a.rehash
return a
end
......
......@@ -90,7 +90,7 @@ module Bio
# class MyMapThing
# include Bio::Map::ActsLikeMap
#
# def initialize (name)
# def initialize(name)
# @name = name
# @mappings_as_maps = Array.new
# end
......@@ -177,7 +177,7 @@ module Bio
# class MyMarkerThing
# include Bio::Map::ActsLikeMarker
#
# def initialize (name)
# def initialize(name)
# @name = name
# @mappings_as_marker = Array.new
# end
......@@ -301,7 +301,7 @@ module Bio
# * _map_: a Bio::Map::SimpleMap object
# * _marker_: a Bio::Map::Marker object
# * _location_: a Bio::Locations object
def initialize (map, marker, location = nil)
def initialize(map, marker, location = nil)
@map, @marker, @location = map, marker, location
end
attr_accessor :map, :marker, :location
......@@ -350,7 +350,7 @@ module Bio
# * type: type of the map (e.g. linkage, radiation_hybrid, cytogenetic, ...)
# * units: unit of the map (e.g. cM, cR, ...)
# *Returns*:: new Bio::Map::SimpleMap object
def initialize (name = nil, type = nil, length = nil, units = nil)
def initialize(name = nil, type = nil, length = nil, units = nil)
@name, @type, @length, @units = name, type, length, units
@mappings_as_map = Array.new
end
......
......@@ -82,7 +82,7 @@ module Bio::Shell
rep << "Codon usage :\n"
hash = Hash.new("0.0%")
seq.codon_usage.sort.each do |codon, num|
percent = format("%.1f%", 100.0 * num / (seq.length / 3))
percent = format("%.1f%%", 100.0 * num / (seq.length / 3))
hash[codon] = percent
end
rep << codontable(1, hash).output
......
......@@ -151,7 +151,7 @@ class CalculatedCuts
def remove_incomplete_cuts(size=nil)
@strands_for_display_current = false
@size = size if size
raise IndexError, "Size of the strand must be provided here or during initalization." if !@size.kind_of?(Fixnum) and not @circular
raise IndexError, "Size of the strand must be provided here or during initalization." if !@size.kind_of?(Integer) and not @circular
vcuts = @vc_primary + @vc_complement
hcuts = @hc_between_strands
......
......@@ -278,6 +278,8 @@ module Bio
# human readable report
def report
# raise NomethodError for compatibility
raise NoMethodError if !defined?(@top_strand) || !@top_strand
report = "### shRNA\n"
report << "Top strand shRNA (#{@top_strand.length} nt):\n"
report << " 5'-#{@top_strand.upcase}-3'\n"
......
......@@ -10,7 +10,7 @@
module Bio
# BioRuby version (Array containing Integer)
BIORUBY_VERSION = [1, 5, 1].extend(Comparable).freeze
BIORUBY_VERSION = [1, 5, 2].extend(Comparable).freeze
# Extra version specifier (String or nil).
# Existance of the value indicates development version.
......
......@@ -628,9 +628,9 @@ module Bio
def test_seqclass_when_seqclass_set
alignment = Alignment.new
alignment.seqclass = Fixnum
alignment.seqclass = Integer
alignment << "this doesn't really make sense"
assert_equal(Fixnum, alignment.seqclass)
assert_equal(Integer, alignment.seqclass)
end
# Alignment#gap_char
......
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