absee 1.0 → 1.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/lib/absee.rb +10 -4
- metadata +9 -12
checksums.yaml
ADDED
|
@@ -0,0 +1,7 @@
|
|
|
1
|
+
---
|
|
2
|
+
SHA1:
|
|
3
|
+
metadata.gz: 4963ba45850feb06cffd7a0aaf3c24514fbe49cd
|
|
4
|
+
data.tar.gz: 341d131db9e2539ecd398dd58f15ab4e2c6645d4
|
|
5
|
+
SHA512:
|
|
6
|
+
metadata.gz: f6954b89ae307421c24807d7f6b0acf57d81d74bcf91784985abd0fd7a03c8981769a81aeb78b54b9499404f3c5b8164d9bf73475053836f5e0072891d6eb213
|
|
7
|
+
data.tar.gz: '033698b4ab7bdcae9a1578e61b1f865d6a86191b6f3aa9b946d4726ba1528b047901d02c6fa42b06c9a80c869f8c446082c67a3492e0a34a2d3471f032bb3118'
|
data/lib/absee.rb
CHANGED
|
@@ -31,8 +31,15 @@ class ABSee
|
|
|
31
31
|
#== Returns:
|
|
32
32
|
# Six arrays: trace data for A, C, G, T, called sequence, and peak indexes
|
|
33
33
|
def read(filename)
|
|
34
|
-
|
|
35
|
-
|
|
34
|
+
if filename.instance_of?(StringIO) or filename.instance_of?(File)
|
|
35
|
+
abFile = filename
|
|
36
|
+
elsif filename.instance_of? String
|
|
37
|
+
#opens ab1 as a File object
|
|
38
|
+
abFile = open(filename)
|
|
39
|
+
else
|
|
40
|
+
raise "Don't know what to do with input type #{filename.class}"
|
|
41
|
+
end
|
|
42
|
+
|
|
36
43
|
byteArray = ""
|
|
37
44
|
#// here we read the first four bytes. It is important
|
|
38
45
|
#// to remember that we do not seek back the file, just
|
|
@@ -48,10 +55,9 @@ class ABSee
|
|
|
48
55
|
end
|
|
49
56
|
|
|
50
57
|
|
|
51
|
-
|
|
52
58
|
##accessors
|
|
53
59
|
#== Returns:
|
|
54
|
-
# the trace data for adenine
|
|
60
|
+
# an array with the trace data for adenine
|
|
55
61
|
def get_traceA()
|
|
56
62
|
return @traceA
|
|
57
63
|
end
|
metadata
CHANGED
|
@@ -1,8 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: absee
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: '1.
|
|
5
|
-
prerelease:
|
|
4
|
+
version: '1.1'
|
|
6
5
|
platform: ruby
|
|
7
6
|
authors:
|
|
8
7
|
- Jenny Cheng
|
|
@@ -11,8 +10,8 @@ bindir: bin
|
|
|
11
10
|
cert_chain: []
|
|
12
11
|
date: 2012-11-14 00:00:00.000000000 Z
|
|
13
12
|
dependencies: []
|
|
14
|
-
description: .ab1 reader / ABIF reader; extracts the peak indexes, called sequence,
|
|
15
|
-
quality scores, and ACGT values from sequencing files
|
|
13
|
+
description: ".ab1 reader / ABIF reader; extracts the peak indexes, called sequence,
|
|
14
|
+
quality scores, and ACGT values from sequencing files"
|
|
16
15
|
email: jencheng@ginkgobioworks.com
|
|
17
16
|
executables: []
|
|
18
17
|
extensions: []
|
|
@@ -22,27 +21,25 @@ files:
|
|
|
22
21
|
homepage: http://rubygems.org/gems/absee
|
|
23
22
|
licenses:
|
|
24
23
|
- MIT
|
|
24
|
+
metadata: {}
|
|
25
25
|
post_install_message:
|
|
26
26
|
rdoc_options: []
|
|
27
27
|
require_paths:
|
|
28
28
|
- lib
|
|
29
29
|
required_ruby_version: !ruby/object:Gem::Requirement
|
|
30
|
-
none: false
|
|
31
30
|
requirements:
|
|
32
|
-
- -
|
|
31
|
+
- - ">="
|
|
33
32
|
- !ruby/object:Gem::Version
|
|
34
33
|
version: 1.9.3
|
|
35
34
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
|
36
|
-
none: false
|
|
37
35
|
requirements:
|
|
38
|
-
- -
|
|
36
|
+
- - ">="
|
|
39
37
|
- !ruby/object:Gem::Version
|
|
40
38
|
version: '0'
|
|
41
39
|
requirements: []
|
|
42
40
|
rubyforge_project:
|
|
43
|
-
rubygems_version:
|
|
41
|
+
rubygems_version: 2.6.11
|
|
44
42
|
signing_key:
|
|
45
|
-
specification_version:
|
|
46
|
-
summary: .ab1 reader / ABIF reader
|
|
43
|
+
specification_version: 4
|
|
44
|
+
summary: ".ab1 reader / ABIF reader"
|
|
47
45
|
test_files: []
|
|
48
|
-
has_rdoc:
|