ms-error_rate 0.0.11 → 0.0.12
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- data/VERSION +1 -1
- data/bin/mascot_pepxml_to_peptide_hit_qvalues.rb +18 -7
- data/lib/ms/error_rate/qvalue.rb +0 -1
- metadata +3 -5
- data/bin/fasta_to_protein_length.rb +0 -20
data/VERSION
CHANGED
@@ -1 +1 @@
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|
1
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-
0.0.
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1
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+
0.0.12
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@@ -6,6 +6,12 @@ require 'set'
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|
6
6
|
|
7
7
|
require 'ms/ident/pepxml'
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8
8
|
require 'ms/ident/peptide_hit/qvalue'
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9
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+
require 'ms/error_rate/qvalue'
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10
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+
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11
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+
def putsv(*args)
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12
|
+
puts(*args) if $VERBOSE
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13
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+
$stdout.flush
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14
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+
end
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9
15
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|
10
16
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EXT = Ms::Ident::PeptideHit::Qvalue::FILE_EXTENSION
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11
17
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combine_base = "combined"
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@@ -32,33 +38,38 @@ $VERBOSE = opt.delete(:verbose)
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|
32
38
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33
39
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files = ARGV.to_a
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34
40
|
|
35
|
-
files.each_slice(2).map
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41
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+
(files=files.each_slice(2).map(&:reverse).flatten) if opt[:decoy_first]
|
36
42
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|
37
43
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groups_of_search_hits = files.map do |file|
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38
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-
|
44
|
+
putsv "reading search hits: #{file}"
|
45
|
+
Ms::Ident::Pepxml.simple_search_hits(file)
|
39
46
|
end
|
40
47
|
|
41
48
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to_run = {}
|
42
49
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if opt[:combine]
|
50
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+
putsv "combining all target hits together and all decoy hits together"
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43
51
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all_target = [] ; all_decoy = []
|
44
52
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groups_of_search_hits.each_slice(2) do |target_hits,decoy_hits|
|
45
53
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all_target.push(*target_hits) ; all_decoy.push(*decoy_hits)
|
46
54
|
end
|
47
|
-
to_run[combine_base] = [all_target, all_decoy]
|
55
|
+
to_run[combine_base + EXT] = [all_target, all_decoy]
|
48
56
|
else
|
49
|
-
groups_of_search_hits.each_slice(2)
|
50
|
-
|
57
|
+
files.zip(groups_of_search_hits).each_slice(2) do |pair_of_file_and_hit_pairs|
|
58
|
+
(tfile_hits, dfile_hits) = pair_of_file_and_hit_pairs
|
59
|
+
file = tfile_hits.first
|
60
|
+
to_run[file.chomp(File.extname(file)) + EXT] = [tfile_hits.last, dfile_hits.last]
|
51
61
|
end
|
52
62
|
end
|
53
63
|
|
54
64
|
to_run.each do |file, target_decoy_pair|
|
55
|
-
|
65
|
+
putsv "calculating qvalues for #{file}"
|
66
|
+
hit_qvalue_pairs = Ms::ErrorRate::Qvalue.target_decoy_qvalues(target_decoy_pair.first, target_decoy_pair.last, :z_together => opt[:z_together]) {|hit| hit.search_scores[:ionscore] }
|
56
67
|
hits = [] ; qvals = []
|
57
68
|
hit_qvalue_pairs.each do |hit, qval|
|
58
69
|
hits << hit ; qvals << qval
|
59
70
|
end
|
60
71
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outfile = Ms::Ident::PeptideHit::Qvalue.to_file(file, hits, qvals)
|
61
|
-
|
72
|
+
putsv "created: #{outfile}"
|
62
73
|
end
|
63
74
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|
64
75
|
|
data/lib/ms/error_rate/qvalue.rb
CHANGED
metadata
CHANGED
@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
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|
5
5
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segments:
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6
6
|
- 0
|
7
7
|
- 0
|
8
|
-
-
|
9
|
-
version: 0.0.
|
8
|
+
- 12
|
9
|
+
version: 0.0.12
|
10
10
|
platform: ruby
|
11
11
|
authors:
|
12
12
|
- John Prince
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@@ -14,7 +14,7 @@ autorequire:
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|
14
14
|
bindir: bin
|
15
15
|
cert_chain: []
|
16
16
|
|
17
|
-
date: 2011-03-
|
17
|
+
date: 2011-03-31 00:00:00 -06:00
|
18
18
|
default_executable:
|
19
19
|
dependencies:
|
20
20
|
- !ruby/object:Gem::Dependency
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@@ -95,7 +95,6 @@ executables:
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|
95
95
|
- fasta_to_nuclear.rb
|
96
96
|
- fasta_to_peptide_centric_db.rb
|
97
97
|
- fasta_to_phobius.rb
|
98
|
-
- fasta_to_protein_length.rb
|
99
98
|
- generate_sbv_input_hashes.rb
|
100
99
|
- mascot_pepxml_to_peptide_hit_qvalues.rb
|
101
100
|
- phobius_to_nontransmembrane.rb
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@@ -117,7 +116,6 @@ files:
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|
117
116
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- bin/fasta_to_nuclear.rb
|
118
117
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- bin/fasta_to_peptide_centric_db.rb
|
119
118
|
- bin/fasta_to_phobius.rb
|
120
|
-
- bin/fasta_to_protein_length.rb
|
121
119
|
- bin/generate_sbv_input_hashes.rb
|
122
120
|
- bin/mascot_pepxml_to_peptide_hit_qvalues.rb
|
123
121
|
- bin/phobius_to_nontransmembrane.rb
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@@ -1,20 +0,0 @@
|
|
1
|
-
#!/usr/bin/env ruby
|
2
|
-
|
3
|
-
if ARGV.size == 0
|
4
|
-
puts "usage: #{File.basename(__FILE__)} <file>.fasta ..."
|
5
|
-
puts "output: <file>.protid_to_size.yml"
|
6
|
-
exit
|
7
|
-
end
|
8
|
-
|
9
|
-
ARGV.each do |file|
|
10
|
-
base = file.chomp(File.extname(file))
|
11
|
-
outfile = base + ".protid_to_size.yml"
|
12
|
-
cnt = 0
|
13
|
-
File.open(outfile,'w') do |out|
|
14
|
-
Ms::Fasta.foreach(file) do |entry|
|
15
|
-
out.puts "#{entry.entry_id}: #{entry.sequence.size}"
|
16
|
-
cnt += 1
|
17
|
-
end
|
18
|
-
end
|
19
|
-
puts "wrote #{cnt} protein lengths to: #{outfile}"
|
20
|
-
end
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