rbbt-sources 3.1.47 → 3.1.48

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checksums.yaml CHANGED
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@@ -204,7 +204,6 @@ module BioMart
204
204
  missing+=v if Organism.compare_archives(current_archive, t) == -1
205
205
  elsif k=~ /^>(.*)/
206
206
  t = $1.strip
207
- iii [current_archive, t, Organism.compare_archives(current_archive, t)]
208
207
  missing+=v if Organism.compare_archives(current_archive, t) == 1
209
208
  end
210
209
  end
@@ -52,24 +52,35 @@ module Ensembl
52
52
  File.join("ftp://" + SERVER, ftp_directory_for(organism) )
53
53
  end
54
54
 
55
- def self.url_for(organism, table)
56
- "#{base_url(organism)}/#{table}.txt.gz.bz2"
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
+
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 = CMD.cmd("wget '#{base_url(organism)}/#{File.basename(base_url(organism))}.sql.gz.bz2' -O -| bunzip2| gunzip").read
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 = CMD.cmd("wget '#{base_url(organism)}/#{File.basename(base_url(organism))}.sql.gz.bz2' -O -| bunzip2| gunzip").read
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
- tsv = TSV.open(CMD.cmd("wget '#{url}' -O - |bunzip2|gunzip", :pipe => true), options)
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 = - phase if utr5 == 0
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: 3.1.47
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: 2020-07-14 00:00:00.000000000 Z
11
+ date: 2020-08-12 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: rbbt-util