bix 0.0.3 → 0.0.5
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- data/lib/bix.rb +1 -0
- data/lib/bix/fastq.rb +6 -1
- data/lib/bix/gtf.rb +73 -0
- metadata +3 -2
data/lib/bix.rb
CHANGED
data/lib/bix/fastq.rb
CHANGED
@@ -11,10 +11,15 @@ module Bix
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11
11
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def from_io(io)
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12
12
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@header = io.gets
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13
13
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@seq = io.gets
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14
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-
io.gets #
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14
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+
io.gets # Throw away + line
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15
15
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@qual = io.gets
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16
16
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17
17
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return false if @header == nil || @seq == nil || @qual == nil
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18
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+
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19
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+
@header.chomp!
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20
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+
@seq.chomp!
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21
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+
@qual.chomp!
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22
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+
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18
23
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return true
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19
24
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end
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20
25
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data/lib/bix/gtf.rb
ADDED
@@ -0,0 +1,73 @@
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1
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+
require 'csv'
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2
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+
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3
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+
module Bix
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4
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+
class Gtf
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5
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+
attr_accessor :chr, :prog, :feature, :start, :stop, :score, :strand, :frame, :props
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6
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+
|
7
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+
def from_line(line)
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8
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+
f = line.chomp.split("\t", -1)
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9
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+
@chr = f[0]
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10
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+
@prog = f[1]
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11
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+
@feature = f[2]
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12
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+
@start = f[3].to_i
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13
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+
raise if @start < 1
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14
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+
@stop = f[4].to_i
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15
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+
raise if @stop < 1
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16
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+
@score = f[5].to_f
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17
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+
@strand = f[6]
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18
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+
raise if @strand.size > 1
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19
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+
@frame = f[7].to_i
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20
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+
|
21
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+
group = f[8]
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22
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+
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23
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+
group.gsub!(/; /, " ") # Remove semicolons
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24
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+
group.gsub!(/;$/, "") # Remove semicolons
|
25
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+
f = CSV::parse_line(group, :col_sep => ' ')
|
26
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+
raise "Unexpected number of fields in group: '#{f[7]}'" unless f.size % 2 == 0
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27
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+
|
28
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+
@props = {}
|
29
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+
while f.size > 0
|
30
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+
key = f.shift
|
31
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+
value = f.shift
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32
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+
|
33
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+
@props[key] = value
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34
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+
end
|
35
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+
end
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36
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+
|
37
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+
# E.g. to get all exons
|
38
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+
def self.get_all(io, feature_regex=//)
|
39
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+
gtfs = []
|
40
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+
for line in io
|
41
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+
g = Gtf.new
|
42
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+
g.from_line(line)
|
43
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+
if g.feature =~ feature_regex
|
44
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+
gtfs << g
|
45
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+
end
|
46
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+
end
|
47
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+
return gtfs
|
48
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+
end
|
49
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+
|
50
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+
def self.get_all_by_prop(io, prop_key, feature_regex=//)
|
51
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+
gtfs = get_all(io, feature_regex)
|
52
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+
gtfs_by_key = {}
|
53
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+
for g in gtfs
|
54
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+
gtfs_by_key[g.props[prop_key]] ||= []
|
55
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+
gtfs_by_key[g.props[prop_key]] << g
|
56
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+
end
|
57
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+
return gtfs_by_key
|
58
|
+
end
|
59
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+
|
60
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+
def to_s
|
61
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+
propstr = ""
|
62
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+
i = 0
|
63
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+
for key, value in @props
|
64
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+
if i > 0
|
65
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+
propstr << " "
|
66
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+
end
|
67
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+
propstr << "#{key} \"#{value}\";"
|
68
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+
i += 1
|
69
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+
end
|
70
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+
return [@chr, @prog, @feature, @start, @stop, @score, @strand, @frame, propstr].join("\t")
|
71
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+
end
|
72
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+
end
|
73
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+
end
|
metadata
CHANGED
@@ -2,7 +2,7 @@
|
|
2
2
|
name: bix
|
3
3
|
version: !ruby/object:Gem::Version
|
4
4
|
prerelease:
|
5
|
-
version: 0.0.
|
5
|
+
version: 0.0.5
|
6
6
|
platform: ruby
|
7
7
|
authors:
|
8
8
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- Jesse Rodriguez
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@@ -10,7 +10,7 @@ autorequire:
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|
10
10
|
bindir: bin
|
11
11
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cert_chain: []
|
12
12
|
|
13
|
-
date:
|
13
|
+
date: 2012-02-29 00:00:00 Z
|
14
14
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dependencies:
|
15
15
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- !ruby/object:Gem::Dependency
|
16
16
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name: swak
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@@ -58,6 +58,7 @@ files:
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|
58
58
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- lib/bix/fasta.rb
|
59
59
|
- lib/bix/fastq.rb
|
60
60
|
- lib/bix/blast.rb
|
61
|
+
- lib/bix/gtf.rb
|
61
62
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homepage: https://github.com/jesserod/bixruby
|
62
63
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licenses: []
|
63
64
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