rbbt-sources 3.1.47 → 3.1.48
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- checksums.yaml +4 -4
- data/lib/rbbt/sources/biomart.rb +0 -1
- data/lib/rbbt/sources/ensembl_ftp.rb +19 -7
- data/share/install/Organism/organism_helpers.rb +6 -1
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 92bb6e2852266c73666e0b07221484822441d19603b2ce9d4fe9ceb6faa44d37
|
4
|
+
data.tar.gz: 9eda4d907bb34ae5b5b95dbdb972b6c659111b042c5b68661d41cf3ccd93e3b8
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 4ac47f700cfc54144bfbc2dc7b3eeaf2e9dce885ccfc1e47c26d978a79dd02d99802a83a888bb1bd80de96ecf9bf023ae548041f3b1867308228c319777dabd4
|
7
|
+
data.tar.gz: 05b07ac77a194f0ad87a36b050eb97d2285490974d0bca039c2163d762c11461f4ccf6c4585df62b24298524bb9f02e4d1d65dae51418e491644b4725fbd864f
|
data/lib/rbbt/sources/biomart.rb
CHANGED
@@ -204,7 +204,6 @@ module BioMart
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|
204
204
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missing+=v if Organism.compare_archives(current_archive, t) == -1
|
205
205
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elsif k=~ /^>(.*)/
|
206
206
|
t = $1.strip
|
207
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-
iii [current_archive, t, Organism.compare_archives(current_archive, t)]
|
208
207
|
missing+=v if Organism.compare_archives(current_archive, t) == 1
|
209
208
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end
|
210
209
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end
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@@ -52,24 +52,35 @@ module Ensembl
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|
52
52
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File.join("ftp://" + SERVER, ftp_directory_for(organism) )
|
53
53
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end
|
54
54
|
|
55
|
-
def self.url_for(organism, table)
|
56
|
-
|
55
|
+
def self.url_for(organism, table, extension)
|
56
|
+
File.join(base_url(organism), table) + ".#{extension}.gz"
|
57
|
+
end
|
58
|
+
|
59
|
+
def self._get_gz(url)
|
60
|
+
begin
|
61
|
+
CMD.cmd("wget '#{url}' -O - | gunzip").read
|
62
|
+
rescue
|
63
|
+
CMD.cmd("wget '#{url}.bz2' -O - | bunzip2 | gunzip").read
|
64
|
+
end
|
65
|
+
end
|
66
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+
|
67
|
+
def self._get_file(organism, table, extension)
|
68
|
+
url = url_for(organism, table, extension)
|
69
|
+
self._get_gz(url)
|
57
70
|
end
|
58
71
|
|
59
72
|
def self.has_table?(organism, table)
|
60
|
-
sql_file =
|
73
|
+
sql_file = _get_file(organism, File.basename(base_url(organism)), 'sql')
|
61
74
|
! sql_file.match(/^CREATE TABLE .#{table}. \((.*?)^\)/sm).nil?
|
62
75
|
end
|
63
76
|
|
64
77
|
def self.fields_for(organism, table)
|
65
|
-
sql_file =
|
66
|
-
|
78
|
+
sql_file = _get_file(organism, File.basename(base_url(organism)), 'sql')
|
67
79
|
chunk = sql_file.match(/^CREATE TABLE .#{table}. \((.*?)^\)/sm)[1]
|
68
80
|
chunk.scan(/^\s+`(.*?)`/).flatten
|
69
81
|
end
|
70
82
|
|
71
83
|
def self.ensembl_tsv(organism, table, key_field = nil, fields = nil, options = {})
|
72
|
-
url = url_for(organism, table)
|
73
84
|
if key_field and fields
|
74
85
|
all_fields = fields_for(organism, table)
|
75
86
|
key_pos = all_fields.index key_field
|
@@ -78,7 +89,8 @@ module Ensembl
|
|
78
89
|
options[:key_field] = key_pos
|
79
90
|
options[:fields] = field_pos
|
80
91
|
end
|
81
|
-
|
92
|
+
|
93
|
+
tsv = TSV.open(StringIO.new(_get_file(organism, table, "txt")), options)
|
82
94
|
tsv.key_field = key_field
|
83
95
|
tsv.fields = fields
|
84
96
|
tsv
|
@@ -728,13 +728,18 @@ file 'protein_sequence' => ["transcripts", "transcript_5utr", "transcript_3utr",
|
|
728
728
|
transcript_sequence.through do |transcript, sequence|
|
729
729
|
protein = transcript_protein[transcript]
|
730
730
|
next if protein.nil? or protein.empty?
|
731
|
+
|
731
732
|
utr5 = transcript_5utr[transcript]
|
732
733
|
utr3 = transcript_3utr[transcript]
|
733
734
|
phase = transcript_phase[transcript] || 0
|
735
|
+
|
734
736
|
if phase < 0
|
735
|
-
utr5
|
737
|
+
if utr5.nil? || utr5 == 0 || utr5 == "0"
|
738
|
+
utr5 = 0
|
739
|
+
end
|
736
740
|
phase = 0
|
737
741
|
end
|
742
|
+
|
738
743
|
psequence = Bio::Sequence::NA.new(("N" * phase) << sequence[utr5..sequence.length-utr3-1]).translate
|
739
744
|
protein_sequence[protein]=psequence
|
740
745
|
end
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rbbt-sources
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 3.1.
|
4
|
+
version: 3.1.48
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2020-
|
11
|
+
date: 2020-08-12 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rbbt-util
|