diadem 0.0.3 → 0.0.4
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- checksums.yaml +4 -4
- data/lib/diadem/cubic.rb +6 -2
- data/lib/diadem/cubic/commandline.rb +6 -2
- data/lib/diadem/version.rb +1 -1
- metadata +2 -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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SHA1:
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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: 6fa16a3c524c7225ef4f4be890f0b1af8073bd7d
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4
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+
data.tar.gz: 927b682e29c08ae8bae24be3f10a1e73fa1d8977
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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: 2106d9d8d5811d48b213e0798e5c2066c16a3f8e8667b103362a3c72b6248f0e6a728b4c72e7e75ece5ac84a5fa222b82d9dc22050b1689559529a1cc2ede63b
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7
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+
data.tar.gz: 81b9d70759379eedc3adb9854e05d6782a926fd204bead5ea88a1c19a583807150140777a2a54752326eb627657eba0c687ee99db5fede5e1287e1a81053c54e
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data/lib/diadem/cubic.rb
CHANGED
@@ -31,7 +31,8 @@ module Diadem
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31
31
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isotopomers = *opt.num_isotopomers.times.map {|n| "M#{n}" }
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32
32
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cats.push(*isotopomers)
|
33
33
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isotopomers.each do |label|
|
34
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-
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34
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+
lowest_coeff = opt.return_zero_coeff ? 0 : 1
|
35
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+
(opt.degree).downto(lowest_coeff) do |coeff|
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35
36
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cats << [label, "coeff", coeff].join("_")
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36
37
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end
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37
38
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end
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@@ -39,6 +40,7 @@ module Diadem
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39
40
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end
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40
41
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41
42
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aaseqs.compact! # ignore blank lines
|
43
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+
aaseqs.uniq! if opt.remove_duplicates
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42
44
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|
43
45
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aaseqs.each do |aaseq|
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44
46
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# we cannot ensure the base 0% has been included in the range, so
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@@ -69,7 +71,9 @@ module Diadem
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69
71
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line = [aaseq, modinfo, info.formula, info.formula.mass.round(6), info.penetration]
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70
72
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line.push *zero_pct_dist.intensities[0,opt.num_isotopomers].map {|v| v.round(6) }
|
71
73
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polynomials.each do |coeffs|
|
72
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-
|
74
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+
rev_coeffs = coeffs.reverse
|
75
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+
rev_coeffs.pop unless opt.return_zero_coeff
|
76
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+
line.push *rev_coeffs
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73
77
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end
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74
78
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out.puts line.join(opt.delim)
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75
79
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end
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@@ -22,6 +22,8 @@ module Diadem
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22
22
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degree: 3,
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23
23
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header: true,
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24
24
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num_isotopomers: 5,
|
25
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+
zero: false,
|
26
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+
remove_duplicates: true,
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25
27
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} )
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26
28
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|
27
29
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parser = OptionParser.new do |op|
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@@ -37,11 +39,13 @@ module Diadem
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37
39
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op.separator "options:"
|
38
40
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op.on("-e", "--element <#{opt.element}>", "element with isotopic label") {|v| opt.element = v.to_sym }
|
39
41
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op.on("-m", "--mass-number <#{opt.mass_number}>", Integer, "the labeled element mass number") {|v| opt.mass_number = v }
|
40
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-
op.on("--no-carbamidomethyl", "
|
42
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+
op.on("--[no-]carbamidomethyl", "default: carbamidomethyl = true") {|v| opt.carbamidomethyl = v }
|
41
43
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op.on("--range <start:stop:step>", "the underlying input values (#{[start, stop, step].join(':')})") {|v| opt.range = make_range[ *v.split(':') ] }
|
42
44
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op.on("--degree <#{opt.degree}>", Integer, "the degree polynomial") {|v| opt.degree = v }
|
43
45
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op.on("--num-isotopomers <#{opt.num_isotopomers}>", Integer, "the number of isotopomers to calculate") {|v| opt.num_isotopomers = v }
|
44
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-
op.on("--no-header", "
|
46
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+
op.on("--[no-]header", "print header line, default: true") {|v| opt.header = v }
|
47
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+
op.on("--return-zero-coeff", "return the 0th polyfit coefficient") {|v| opt.return_zero_coeff = v }
|
48
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+
op.on("--[no-]remove-duplicates", "disregard duplicate peptide entries, default: true") {|v| opt.remove_duplicates = v }
|
45
49
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end
|
46
50
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parser.parse!(argv)
|
47
51
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if argv.size == 0
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data/lib/diadem/version.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: diadem
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3
3
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version: !ruby/object:Gem::Version
|
4
|
-
version: 0.0.
|
4
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+
version: 0.0.4
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5
5
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platform: ruby
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6
6
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authors:
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7
7
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- John Prince
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8
8
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autorequire:
|
9
9
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bindir: bin
|
10
10
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cert_chain: []
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11
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-
date: 2013-
|
11
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+
date: 2013-11-07 00:00:00.000000000 Z
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12
12
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dependencies:
|
13
13
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- !ruby/object:Gem::Dependency
|
14
14
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name: mspire
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