transrate 1.0.0.beta4 → 1.0.0.beta5

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data/README.md CHANGED
@@ -28,7 +28,7 @@ This software is being actively developed. Please be aware that there may be bug
28
28
 
29
29
  ## Citation
30
30
 
31
- Transrate is pre-publication academic software. If you use it, please cite the github repository and the DOI: [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.13161.svg)](http://dx.doi.org/10.5281/zenodo.13161).
31
+ Transrate is pre-publication academic software. If you use it, please cite the github repository and the DOI: [![DOI](https://zenodo.org/badge/3687/Blahah/transrate.svg)](http://dx.doi.org/10.5281/zenodo.18325).
32
32
 
33
33
  ## Documentation
34
34
 
data/bin/transrate CHANGED
@@ -4,6 +4,7 @@ require 'trollop'
4
4
  require 'transrate'
5
5
  require 'csv'
6
6
  require 'bindeps'
7
+ require 'colorize'
7
8
 
8
9
  include Transrate
9
10
 
@@ -27,9 +28,19 @@ module Kernel
27
28
  end
28
29
  end
29
30
 
31
+ txp = '░▓▓▓^▓▓▓░'
32
+ toptxp = txp.green
33
+ midtxp = txp.yellow
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+ bottxp = txp.red
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+
30
36
  opts = Trollop::options do
31
37
  version Transrate::VERSION::STRING.dup
32
38
  banner <<-EOS
39
+ _ _
40
+ | |_ _ __ __ _ _ __ ___ _ __ __ _ | |_ ___
41
+ #{toptxp} | __|| '__|/ _` || '_ \\ / __|| '__|/ _` || __|/ _ \\ #{toptxp}
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+ #{midtxp} | |_ | | | (_| || | | |\\__ \\| | | (_| || |_| __/ #{midtxp}
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+ #{bottxp} \\__||_| \\__,_||_| |_||___/|_| \\__,_| \\__|\\___| #{bottxp}
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44
 
34
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  Transrate v#{Transrate::VERSION::STRING.dup}
35
46
  by Richard Smith-Unna, Chris Boursnell, Rob Patro,
@@ -38,28 +49,15 @@ opts = Trollop::options do
38
49
  DESCRIPTION:
39
50
  Analyse a de-novo transcriptome assembly using three kinds of metrics:
40
51
 
41
- 1. sequence-based (basic)
42
- 2. read-mapping-based (if --left and --right are provided)
43
- 3. reference-based (if --reference is provided)
52
+ 1. sequence based (if --assembly is given)
53
+ 2. read mapping based (if --left and --right are given)
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+ 3. reference based (if --reference is given)
44
55
 
45
- Bug reports and feature requests at:
46
- http://github.com/blahah/transrate
56
+ Documentation at http://hibberdlab.com/transrate
47
57
 
48
58
  USAGE:
49
59
  transrate <options>
50
60
 
51
- EXAMPLES:
52
- # check dependencies and install any that are missing
53
- transrate --install-deps
54
- # get the transrate score for the assembly and each contig
55
- transrate --assembly contigs.fa --left left.fq --right right.fq
56
- # basic assembly metrics only
57
- transrate --assembly contigs.fa
58
- # basic and reference-based metrics with 8 threads
59
- transrate --assembly contigs.fa --reference Athaliana_transcripts.fa --threads 8
60
- # contig and read-based metrics for two assemblies with 32 threads
61
- transrate --assembly one.fa,two.fa --left l.fq --right r.fq --threads 32
62
-
63
61
  OPTIONS:
64
62
 
65
63
  EOS
@@ -69,22 +67,47 @@ opts = Trollop::options do
69
67
  :type => String
70
68
  opt :right, "Right reads file in FASTQ format",
71
69
  :type => String
72
- opt :reference, "Reference proteome file in FASTA format",
70
+ opt :reference, "Reference proteome or transcriptome file in FASTA format",
73
71
  :type => String
74
72
  opt :threads, "Number of threads to use",
75
73
  :default => 8,
76
74
  :type => Integer
77
- opt :merge_assemblies, "Merge multiple assemblies into file",
75
+ opt :merge_assemblies, "Merge best contigs from multiple assemblies into file",
78
76
  :type => String
79
77
  opt :outfile, "Prefix filename to use for CSV output",
80
78
  :default => 'transrate'
81
- opt :loglevel, "The amount of information to print. " +
79
+ opt :loglevel, "Log level. " +
82
80
  "One of [error, info, warn, debug]",
83
81
  :default => 'info'
84
82
  opt :install_deps, "Install any missing dependencies. One of [all, read, ref]",
85
83
  :type => String, :default => nil
86
- # opt :install_read_deps, "install missing dependencies for read metrics only"
87
- # opt :install_ref_deps, "install missing dependencies for reference metrics only"
84
+ opt :examples, "Show some example commands with explanations"
85
+ end
86
+
87
+ if opts.examples
88
+ puts <<-EOS
89
+
90
+ Transrate v#{Transrate::VERSION::STRING.dup}
91
+
92
+ EXAMPLE COMMANDS:
93
+
94
+ # check dependencies and install any that are missing
95
+ transrate --install-deps
96
+
97
+ # get the transrate score for the assembly and each contig
98
+ transrate --assembly contigs.fa --left left.fq --right right.fq
99
+
100
+ # basic assembly metrics only
101
+ transrate --assembly contigs.fa
102
+
103
+ # basic and reference-based metrics with 8 threads
104
+ transrate --assembly contigs.fa --reference ref.fa --threads 8
105
+
106
+ # contig and read-based metrics for two assemblies with 32 threads
107
+ transrate --assembly one.fa,two.fa --left l.fq --right r.fq --threads 32
108
+
109
+ EOS
110
+ exit(0)
88
111
  end
89
112
 
90
113
  # Check dependencies if they are relevant to the command issued,
data/lib/transrate.rb CHANGED
@@ -37,4 +37,3 @@ require 'transrate/read_metrics'
37
37
  require 'transrate/comparative_metrics'
38
38
  require 'transrate/contig_metrics'
39
39
  require 'transrate/cmd'
40
- require 'transrate/transrate.so'
@@ -11,7 +11,7 @@ module Transrate
11
11
  MAJOR = 1
12
12
  MINOR = 0
13
13
  PATCH = 0
14
- BUILD = 'beta4'
14
+ BUILD = 'beta5'
15
15
 
16
16
  STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')
17
17
  end
data/transrate.gemspec CHANGED
@@ -23,6 +23,7 @@ Gem::Specification.new do |gem|
23
23
  gem.add_dependency 'bio', '~> 1.4', '>= 1.4.3'
24
24
  gem.add_dependency 'crb-blast', '~> 0.6', '>= 0.6.4'
25
25
  gem.add_dependency 'fix-trinity-output', '~> 1.0', '>= 1.0'
26
+ gem.add_dependency 'colorize', '~> 0.7', '>= 0.7.7'
26
27
 
27
28
  gem.add_development_dependency 'rake', '~> 10.3', '>= 10.3.2'
28
29
  gem.add_development_dependency 'rake-compiler', '~> 0.9', '>= 0.9.2'
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: transrate
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.0.0.beta4
4
+ version: 1.0.0.beta5
5
5
  platform: ruby
6
6
  authors:
7
7
  - Richard Smith-Unna
@@ -9,7 +9,7 @@ authors:
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2015-06-05 00:00:00.000000000 Z
12
+ date: 2015-06-11 00:00:00.000000000 Z
13
13
  dependencies:
14
14
  - !ruby/object:Gem::Dependency
15
15
  name: yell
@@ -131,6 +131,26 @@ dependencies:
131
131
  - - ">="
132
132
  - !ruby/object:Gem::Version
133
133
  version: '1.0'
134
+ - !ruby/object:Gem::Dependency
135
+ name: colorize
136
+ requirement: !ruby/object:Gem::Requirement
137
+ requirements:
138
+ - - "~>"
139
+ - !ruby/object:Gem::Version
140
+ version: '0.7'
141
+ - - ">="
142
+ - !ruby/object:Gem::Version
143
+ version: 0.7.7
144
+ type: :runtime
145
+ prerelease: false
146
+ version_requirements: !ruby/object:Gem::Requirement
147
+ requirements:
148
+ - - "~>"
149
+ - !ruby/object:Gem::Version
150
+ version: '0.7'
151
+ - - ">="
152
+ - !ruby/object:Gem::Version
153
+ version: 0.7.7
134
154
  - !ruby/object:Gem::Dependency
135
155
  name: rake
136
156
  requirement: !ruby/object:Gem::Requirement