sequenceserver 1.0.0.pre.4 → 1.0.0.pre.5
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- checksums.yaml +4 -4
- data/bin/sequenceserver +3 -3
- data/lib/sequenceserver/blast/constants.rb +1 -1
- data/lib/sequenceserver/blast/hit.rb +1 -1
- data/lib/sequenceserver/database.rb +1 -1
- data/lib/sequenceserver/sequence.rb +4 -3
- data/sequenceserver.gemspec +2 -1
- metadata +22 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
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---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: e3a82c074774e6df93a1a55e2261c8267cf60048
|
4
|
+
data.tar.gz: 9d5fb2432833c4dc25e472b14fd93200f03f8fe7
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: a4334e199b5dd02c67bdac5352918b840f3c39911583132601682aec5ca215f365f06d9f67494692c258c9075db3a9217fd91b6fa8baa50c5795f8e25bd6071b
|
7
|
+
data.tar.gz: 10e137003e87a4e0aee3c83183dd88dc65948f313186b100188ea0a50b4c644f49b8894ee07ecc53e9161d5eebc28e943b6545c136fc4059a52ccede2fd4fcc0
|
data/bin/sequenceserver
CHANGED
@@ -305,7 +305,7 @@ MSG
|
|
305
305
|
puts e
|
306
306
|
|
307
307
|
# Offer user to format the FASTA files.
|
308
|
-
database_dir = SequenceServer[:database_dir]
|
308
|
+
database_dir = SequenceServer.config[:database_dir]
|
309
309
|
puts
|
310
310
|
puts <<MSG
|
311
311
|
Search for FASTA files (.fa, .fasta, .fna) in '#{database_dir}' and try
|
@@ -344,8 +344,8 @@ MSG
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|
344
344
|
if list_unformatted_fastas? || make_blast_databases?
|
345
345
|
unformatted_fastas = SequenceServer::Database.unformatted_fastas
|
346
346
|
if unformatted_fastas.empty?
|
347
|
-
puts "All FASTA files in #{SequenceServer[:database_dir]}
|
348
|
-
'formatted.'
|
347
|
+
puts "All FASTA files in #{SequenceServer.config[:database_dir]} " \
|
348
|
+
'are formatted.'
|
349
349
|
exit
|
350
350
|
end
|
351
351
|
end
|
@@ -11,7 +11,7 @@ module SequenceServer
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|
11
11
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mismatch positive gapopen gaps ppos frames
|
12
12
|
qframe hframe btop staxids sscinames scomnames
|
13
13
|
sblastnames sskingdoms stitle salltitles sstrand
|
14
|
-
qcovs qcovhsp)
|
14
|
+
qcovs qcovhsp).join(' ')
|
15
15
|
OUTFMT = {
|
16
16
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'pairwise' => [0, :txt],
|
17
17
|
'qa' => [1, :txt],
|
@@ -26,7 +26,7 @@ module SequenceServer
|
|
26
26
|
def links
|
27
27
|
links = Links.instance_methods.map { |m| send m }
|
28
28
|
links.compact!
|
29
|
-
links.sort_by
|
29
|
+
links.sort_by { |link| link[:order] }
|
30
30
|
end
|
31
31
|
|
32
32
|
# Returns an array of database objects which contain the queried sequence
|
@@ -203,7 +203,7 @@ module SequenceServer
|
|
203
203
|
# replaces _ with ' ',
|
204
204
|
db_name.gsub!(/(_)/, ' ')
|
205
205
|
# replaces '.' with ' ' when no numbers are on either side,
|
206
|
-
db_name.gsub!(/(
|
206
|
+
db_name.gsub!(/(\D)\.(?=\D)/, '\1 ')
|
207
207
|
# preserves version numbers
|
208
208
|
db_name.gsub!(/\W*(\d+([.-]\d+)+)\W*/, ' \1 ')
|
209
209
|
db_name
|
@@ -192,9 +192,10 @@ module SequenceServer
|
|
192
192
|
|
193
193
|
logger.debug("Executing: #{command}")
|
194
194
|
|
195
|
-
|
196
|
-
|
197
|
-
|
195
|
+
out = `#{command} 2> /dev/null`
|
196
|
+
@sequences = out.each_line.map do |line|
|
197
|
+
Sequence.new(*line.chomp.split(' '))
|
198
|
+
end
|
198
199
|
extend(IO) && write if in_file
|
199
200
|
end
|
200
201
|
|
data/sequenceserver.gemspec
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
Gem::Specification.new do |s|
|
2
2
|
# meta
|
3
3
|
s.name = 'sequenceserver'
|
4
|
-
s.version = '1.0.0-
|
4
|
+
s.version = '1.0.0-5'
|
5
5
|
s.authors = ['Anurag Priyam', 'Ben J Woodcroft',
|
6
6
|
'Vivek Rai', 'Yannick Wurm']
|
7
7
|
s.email = ['anurag08priyam@gmail.com', 'b.woodcroft@uq.edu.au']
|
@@ -17,6 +17,7 @@ DESC
|
|
17
17
|
# dependencies
|
18
18
|
s.add_dependency('thin', '~> 1.6', '>= 1.6.2')
|
19
19
|
s.add_dependency('sinatra', '~> 1.4', '>= 1.4.5')
|
20
|
+
s.add_dependency('json', '~> 1.8', '>= 1.8.2')
|
20
21
|
s.add_dependency('ox', '~> 2.1', '>= 2.1.1')
|
21
22
|
s.add_dependency('slop', '~> 3.6', '>= 3.6.0')
|
22
23
|
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: sequenceserver
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 1.0.0.pre.
|
4
|
+
version: 1.0.0.pre.5
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Anurag Priyam
|
@@ -11,7 +11,7 @@ authors:
|
|
11
11
|
autorequire:
|
12
12
|
bindir: bin
|
13
13
|
cert_chain: []
|
14
|
-
date: 2015-02-
|
14
|
+
date: 2015-02-21 00:00:00.000000000 Z
|
15
15
|
dependencies:
|
16
16
|
- !ruby/object:Gem::Dependency
|
17
17
|
name: thin
|
@@ -53,6 +53,26 @@ dependencies:
|
|
53
53
|
- - ">="
|
54
54
|
- !ruby/object:Gem::Version
|
55
55
|
version: 1.4.5
|
56
|
+
- !ruby/object:Gem::Dependency
|
57
|
+
name: json
|
58
|
+
requirement: !ruby/object:Gem::Requirement
|
59
|
+
requirements:
|
60
|
+
- - "~>"
|
61
|
+
- !ruby/object:Gem::Version
|
62
|
+
version: '1.8'
|
63
|
+
- - ">="
|
64
|
+
- !ruby/object:Gem::Version
|
65
|
+
version: 1.8.2
|
66
|
+
type: :runtime
|
67
|
+
prerelease: false
|
68
|
+
version_requirements: !ruby/object:Gem::Requirement
|
69
|
+
requirements:
|
70
|
+
- - "~>"
|
71
|
+
- !ruby/object:Gem::Version
|
72
|
+
version: '1.8'
|
73
|
+
- - ">="
|
74
|
+
- !ruby/object:Gem::Version
|
75
|
+
version: 1.8.2
|
56
76
|
- !ruby/object:Gem::Dependency
|
57
77
|
name: ox
|
58
78
|
requirement: !ruby/object:Gem::Requirement
|