ruby-igv 0.0.4 → 0.0.5
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/README.md +5 -3
- data/lib/igv.rb +14 -9
- data/lib/igv/version.rb +3 -1
- metadata +6 -6
checksums.yaml
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
---
|
|
2
2
|
SHA256:
|
|
3
|
-
metadata.gz:
|
|
4
|
-
data.tar.gz:
|
|
3
|
+
metadata.gz: a162dd0aa5d26fd45b3da87eb9c8e4faec6bc47f6922dc850dc5f5f556405c26
|
|
4
|
+
data.tar.gz: 6ceb747c0f8b5b697f561c2836c8e021d29fd2bcc0cc5bc91cc7916bc24b0c61
|
|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: 0e05cd137522d371629790616283c5f2c31f96f9882979d64f46ab83530ccf14569bc039213ddda103653ad009d9818e50f1e95e5f3738cb985903da6d8c6ed2
|
|
7
|
+
data.tar.gz: 361d5f9e770f4f78304e4b99672e6e5e2c116bd8994b5d57076b808b40b27ae5fa493c74842923d4165adef2b79827ae85e5d711d9ce279f001afddb0676df95
|
data/README.md
CHANGED
|
@@ -4,9 +4,7 @@
|
|
|
4
4
|
[](https://rubydoc.info/gems/ruby-igv)
|
|
5
5
|
[](LICENSE.txt)
|
|
6
6
|
|
|
7
|
-
|
|
8
|
-
|
|
9
|
-
Based on [brentp/bio-playground/igv](https://github.com/brentp/bio-playground).
|
|
7
|
+
Controlling [Integrative Genomics Viewer (IGV)](http://software.broadinstitute.org/software/igv/) with the [Ruby](https://github.com/ruby/ruby) language.
|
|
10
8
|
|
|
11
9
|
## Installation
|
|
12
10
|
|
|
@@ -37,6 +35,10 @@ igv.send 'echo' # whatever you want
|
|
|
37
35
|
* Write, clarify, or fix documentation
|
|
38
36
|
* Suggest or add new features
|
|
39
37
|
|
|
38
|
+
# Acknowledgement
|
|
39
|
+
This gem is strongly inspired by a Python script developed by Brent Pedersen.
|
|
40
|
+
* [brentp/bio-playground/igv](https://github.com/brentp/bio-playground).
|
|
41
|
+
|
|
40
42
|
## License
|
|
41
43
|
|
|
42
44
|
The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
|
data/lib/igv.rb
CHANGED
|
@@ -1,11 +1,16 @@
|
|
|
1
|
+
# frozen_string_literal: true
|
|
2
|
+
|
|
1
3
|
require 'igv/version'
|
|
2
4
|
require 'socket'
|
|
3
5
|
require 'fileutils'
|
|
4
6
|
|
|
7
|
+
# The Integrative Genomics Viewer (IGV)
|
|
8
|
+
# https://software.broadinstitute.org/software/igv/
|
|
5
9
|
class IGV
|
|
6
10
|
class Error < StandardError; end
|
|
7
11
|
|
|
8
12
|
attr_reader :host, :port, :snapshot_dir, :history
|
|
13
|
+
|
|
9
14
|
def initialize(host: '127.0.0.1', port: 60_151, snapshot_dir: Dir.pwd)
|
|
10
15
|
@host = host
|
|
11
16
|
@port = port
|
|
@@ -25,24 +30,24 @@ class IGV
|
|
|
25
30
|
end
|
|
26
31
|
|
|
27
32
|
def go(position)
|
|
28
|
-
send
|
|
33
|
+
send "goto #{position}"
|
|
29
34
|
end
|
|
30
35
|
alias goto go
|
|
31
36
|
|
|
32
37
|
def genome(name_or_path)
|
|
33
38
|
path = File.expand_path(name_or_path)
|
|
34
39
|
if File.exist?(path)
|
|
35
|
-
send
|
|
40
|
+
send "genome #{path}"
|
|
36
41
|
else
|
|
37
|
-
send
|
|
42
|
+
send "genome #{name_or_path}"
|
|
38
43
|
end
|
|
39
44
|
end
|
|
40
45
|
|
|
41
46
|
def load(path_or_url)
|
|
42
47
|
if URI.parse(path_or_url).scheme
|
|
43
|
-
send
|
|
48
|
+
send "load #{path_or_url}"
|
|
44
49
|
else
|
|
45
|
-
send
|
|
50
|
+
send "load #{File.expand_path(path_or_url)}"
|
|
46
51
|
end
|
|
47
52
|
end
|
|
48
53
|
|
|
@@ -51,11 +56,11 @@ class IGV
|
|
|
51
56
|
end
|
|
52
57
|
|
|
53
58
|
def sort(option = 'base')
|
|
54
|
-
|
|
55
|
-
send 'sort ' + option
|
|
56
|
-
else
|
|
59
|
+
unless %w[base position strand quality sample readGroup].include? option
|
|
57
60
|
raise 'options is one of: base, position, strand, quality, sample, and readGroup.'
|
|
58
61
|
end
|
|
62
|
+
|
|
63
|
+
send "sort #{option}"
|
|
59
64
|
end
|
|
60
65
|
|
|
61
66
|
def expand(_track = '')
|
|
@@ -97,7 +102,7 @@ class IGV
|
|
|
97
102
|
# we can set the snapshot dir. then just use the filename.
|
|
98
103
|
dir_path = File.dirname(file_path)
|
|
99
104
|
set_snapshot_dir(File.expand_path(dir_path)) if dir_path != '.'
|
|
100
|
-
send
|
|
105
|
+
send "snapshot #{File.basename(file_path)}"
|
|
101
106
|
else
|
|
102
107
|
send 'snapshot'
|
|
103
108
|
end
|
data/lib/igv/version.rb
CHANGED
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: ruby-igv
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.0.
|
|
4
|
+
version: 0.0.5
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- kojix2
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2020-
|
|
11
|
+
date: 2020-12-10 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: bundler
|
|
@@ -66,7 +66,7 @@ dependencies:
|
|
|
66
66
|
- - ">="
|
|
67
67
|
- !ruby/object:Gem::Version
|
|
68
68
|
version: '0'
|
|
69
|
-
description:
|
|
69
|
+
description: Control IGV (Integrative Genomics Viewer) with Ruby.
|
|
70
70
|
email:
|
|
71
71
|
- 2xijok@gmail.com
|
|
72
72
|
executables: []
|
|
@@ -89,15 +89,15 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
|
89
89
|
requirements:
|
|
90
90
|
- - ">="
|
|
91
91
|
- !ruby/object:Gem::Version
|
|
92
|
-
version: 2.
|
|
92
|
+
version: '2.4'
|
|
93
93
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
|
94
94
|
requirements:
|
|
95
95
|
- - ">="
|
|
96
96
|
- !ruby/object:Gem::Version
|
|
97
97
|
version: '0'
|
|
98
98
|
requirements: []
|
|
99
|
-
rubygems_version: 3.1.
|
|
99
|
+
rubygems_version: 3.1.4
|
|
100
100
|
signing_key:
|
|
101
101
|
specification_version: 4
|
|
102
|
-
summary:
|
|
102
|
+
summary: Control IGV (Integrative Genomics Viewer) with Ruby.
|
|
103
103
|
test_files: []
|