ms-error_rate 0.0.8 → 0.0.9
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- data/VERSION +1 -1
- data/bin/fasta_to_protein_length.rb +20 -0
- data/bin/mascot_pepxml_to_peptide_hit_qvalues.rb +2 -1
- metadata +4 -2
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
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-
0.0.
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1
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+
0.0.9
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@@ -0,0 +1,20 @@
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|
1
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+
#!/usr/bin/env ruby
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2
|
+
|
3
|
+
if ARGV.size == 0
|
4
|
+
puts "usage: #{File.basename(__FILE__)} <file>.fasta ..."
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5
|
+
puts "output: <file>.protid_to_size.yml"
|
6
|
+
exit
|
7
|
+
end
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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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@@ -4,6 +4,7 @@ require 'trollop'
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|
4
4
|
require 'nokogiri'
|
5
5
|
require 'set'
|
6
6
|
|
7
|
+
require 'ms/ident/peptide_hit/qvalue'
|
7
8
|
require 'ms/error_rate/qvalue/pepxml'
|
8
9
|
|
9
10
|
opts = Trollop::Parser.new do
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@@ -30,7 +31,7 @@ files.each_slice(2).map do |target, decoy|
|
|
30
31
|
hit_qvalue_pairs.each do |hit, qval|
|
31
32
|
hits << hit ; qvals << qval
|
32
33
|
end
|
33
|
-
outfile = Ms::Ident::PeptideHit::Qvalue.to_phq(target.chomp(File.
|
34
|
+
outfile = Ms::Ident::PeptideHit::Qvalue.to_phq(target.chomp(File.extname(target)), hits, qvals)
|
34
35
|
puts "created: #{outfile}" if $VERBOSE
|
35
36
|
end
|
36
37
|
|
metadata
CHANGED
@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
|
|
5
5
|
segments:
|
6
6
|
- 0
|
7
7
|
- 0
|
8
|
-
-
|
9
|
-
version: 0.0.
|
8
|
+
- 9
|
9
|
+
version: 0.0.9
|
10
10
|
platform: ruby
|
11
11
|
authors:
|
12
12
|
- John T. Prince
|
@@ -67,6 +67,7 @@ executables:
|
|
67
67
|
- fasta_to_nuclear.rb
|
68
68
|
- fasta_to_peptide_centric_db.rb
|
69
69
|
- fasta_to_phobius.rb
|
70
|
+
- fasta_to_protein_length.rb
|
70
71
|
- generate_sbv_input_hashes.rb
|
71
72
|
- mascot_pepxml_to_peptide_hit_qvalues.rb
|
72
73
|
- phobius_to_nontransmembrane.rb
|
@@ -87,6 +88,7 @@ files:
|
|
87
88
|
- bin/fasta_to_nuclear.rb
|
88
89
|
- bin/fasta_to_peptide_centric_db.rb
|
89
90
|
- bin/fasta_to_phobius.rb
|
91
|
+
- bin/fasta_to_protein_length.rb
|
90
92
|
- bin/generate_sbv_input_hashes.rb
|
91
93
|
- bin/mascot_pepxml_to_peptide_hit_qvalues.rb
|
92
94
|
- bin/phobius_to_nontransmembrane.rb
|