gfa 0.5.0 → 0.6.0
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- checksums.yaml +4 -4
- data/bin/gfa-mean-depth +37 -0
- data/bin/gfa-merge +34 -0
- data/bin/gfa-paths-to-fasta +29 -0
- data/lib/gfa/common.rb +13 -0
- data/lib/gfa/version.rb +1 -1
- metadata +5 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: dc98fa1d3479be3fee554dab64876d6cd42795aec08a6b60be6ccb148c57c679
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4
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+
data.tar.gz: 28ef77ca42b374e58c983f474d44801060dadb2df912230e431cf40ee8f1386c
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 1a7226dbe5813cc9e7b0cde0e756b0b41395d45e690fd3df0e6ad266f51a209d55d72fdaeaab5aaebd3fec7ce033b54bb04510903cc3eadef230bd30485f037e
|
7
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+
data.tar.gz: 32f081a9cf35219f05cb21654011a32a1645f13cbf1d7dda320ebef0b7d893523943cd71f8c9f8a310f1021b6adfaa99b1f863d498be1bbb77bf0a5e04779efd
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data/bin/gfa-mean-depth
ADDED
@@ -0,0 +1,37 @@
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1
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+
#!/usr/bin/env ruby
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2
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+
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3
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+
# @package MiGA
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4
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+
# @license Artistic-2.0
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5
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+
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6
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+
$LOAD_PATH.push File.expand_path('../../lib', __FILE__)
|
7
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+
$LOAD_PATH.push File.expand_path('../../lib', File.realpath(__FILE__))
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8
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+
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9
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+
require 'gfa'
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10
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+
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11
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+
input, threads = ARGV
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12
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+
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13
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+
unless input
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14
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+
$stderr.puts <<~HELP
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15
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+
Calculate the average sequencing depth of all segments in the GFA
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16
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+
weighted by the segment lengths
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17
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+
|
18
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+
gfa-mean-depth <input> [<threads>]
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19
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+
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20
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+
<input> Input GFA file to read
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21
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+
<threads> If passed, parallelize process with these many threads
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22
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+
HELP
|
23
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+
exit(1)
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24
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+
end
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25
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+
|
26
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+
$stderr.puts "Loading GFA: #{input}"
|
27
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+
gfa = GFA.load_parallel(input, (threads || 1).to_i)
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28
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+
|
29
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+
$stderr.puts 'Calculating average depth'
|
30
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+
n = gfa.total_length
|
31
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+
avg =
|
32
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+
gfa.segments.set.map do |segment|
|
33
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+
raise "Some segments are missing depth data" unless segment.DP
|
34
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+
segment.DP.value * segment.length / n
|
35
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+
end.inject(:+)
|
36
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+
puts avg
|
37
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+
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data/bin/gfa-merge
ADDED
@@ -0,0 +1,34 @@
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1
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+
#!/usr/bin/env ruby
|
2
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+
|
3
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+
# @package MiGA
|
4
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+
# @license Artistic-2.0
|
5
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+
|
6
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+
$LOAD_PATH.push File.expand_path('../../lib', __FILE__)
|
7
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+
$LOAD_PATH.push File.expand_path('../../lib', File.realpath(__FILE__))
|
8
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+
|
9
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+
require 'gfa'
|
10
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+
|
11
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+
output = ARGV.shift
|
12
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+
input = ARGV
|
13
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+
|
14
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+
if input.empty?
|
15
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+
$stderr.puts <<~HELP
|
16
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+
Combine several GFAs into a single GFA. Requires uniqueness of element names
|
17
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+
|
18
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+
gfa-merge <output> <input...>
|
19
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+
|
20
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+
<output> Output GFA file to be created
|
21
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+
<input...> List of input GFA files to read
|
22
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+
HELP
|
23
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+
exit(1)
|
24
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+
end
|
25
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+
|
26
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+
gfa = GFA.new
|
27
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+
input.each do |i|
|
28
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+
$stderr.puts "Merging GFA: #{i}"
|
29
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+
gfa.merge! GFA.load(i)
|
30
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+
end
|
31
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+
|
32
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+
$stderr.puts "Saving GFA: #{output}"
|
33
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+
gfa.save(output)
|
34
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+
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@@ -0,0 +1,29 @@
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1
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+
#!/usr/bin/env ruby
|
2
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+
|
3
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+
# @package MiGA
|
4
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+
# @license Artistic-2.0
|
5
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+
|
6
|
+
$LOAD_PATH.push File.expand_path('../../lib', __FILE__)
|
7
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+
$LOAD_PATH.push File.expand_path('../../lib', File.realpath(__FILE__))
|
8
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+
|
9
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+
require 'gfa'
|
10
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+
|
11
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+
input, output, threads = ARGV
|
12
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+
|
13
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+
unless output
|
14
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+
$stderr.puts <<~HELP
|
15
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+
Extract the sequences of the paths from a GFA to FastA file
|
16
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+
|
17
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+
gfa-merge <input> <output> [<threads>]
|
18
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+
|
19
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+
<input> Input GFA file to read
|
20
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+
<output> Output FastA file to be created
|
21
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+
<threads> If passed, parallelize process with these many threads
|
22
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+
HELP
|
23
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+
exit(1)
|
24
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+
end
|
25
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+
|
26
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+
$stderr.puts "Loading GFA: #{input}"
|
27
|
+
gfa = GFA.load_parallel(input, (threads || 1).to_i)
|
28
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+
|
29
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+
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data/lib/gfa/common.rb
CHANGED
@@ -67,4 +67,17 @@ class GFA
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67
67
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def total_length
|
68
68
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segments.total_length
|
69
69
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end
|
70
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+
|
71
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+
##
|
72
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+
# Adds the entrie of +gfa+ to itself
|
73
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+
def merge!(gfa)
|
74
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+
records.each { |k, v| v.merge!(gfa.records[k]) }
|
75
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+
self
|
76
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+
end
|
77
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+
|
78
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+
##
|
79
|
+
# Creates a new GFA based on itself and appends all entries in +gfa+
|
80
|
+
def merge(gfa)
|
81
|
+
GFA.new(opts).merge!(self).merge!(gfa)
|
82
|
+
end
|
70
83
|
end
|
data/lib/gfa/version.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: gfa
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.
|
4
|
+
version: 0.6.0
|
5
5
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platform: ruby
|
6
6
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authors:
|
7
7
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- Luis M. Rodriguez-R
|
8
8
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autorequire:
|
9
9
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bindir: bin
|
10
10
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cert_chain: []
|
11
|
-
date: 2023-
|
11
|
+
date: 2023-10-05 00:00:00.000000000 Z
|
12
12
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dependencies:
|
13
13
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- !ruby/object:Gem::Dependency
|
14
14
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name: rgl
|
@@ -65,6 +65,9 @@ files:
|
|
65
65
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- Rakefile
|
66
66
|
- bin/gfa-add-gaf
|
67
67
|
- bin/gfa-greedy-modules
|
68
|
+
- bin/gfa-mean-depth
|
69
|
+
- bin/gfa-merge
|
70
|
+
- bin/gfa-paths-to-fasta
|
68
71
|
- bin/gfa-subgraph
|
69
72
|
- lib/gfa.rb
|
70
73
|
- lib/gfa/common.rb
|