parse_fasta 2.1.0 → 2.1.1
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- checksums.yaml +4 -4
- data/CHANGELOG.md +4 -0
- data/README.md +10 -2
- data/lib/parse_fasta/record.rb +4 -3
- data/lib/parse_fasta/version.rb +1 -1
- data/spec/parse_fasta/record_spec.rb +2 -2
- 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: 605e579f4970a6c9a7af84c1717b2b381fcbacf9
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4
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+
data.tar.gz: a60a0c7632ef0b316214995fdc7e0b28db8876e1
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SHA512:
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-
metadata.gz:
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-
data.tar.gz:
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6
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+
metadata.gz: a905d2eb000620a7b474279cf1e21863548c18161c2bff6e4a5f82024893dc384462d0eecbfc48a3cde6eaf27c4a72fecd13640b3b77ae5e8111e55d5dcaa014
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7
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+
data.tar.gz: c6b33d1c8e134317bb21ddd59e22ca75740236e2ca97e9f9e1c57e65e51e645451c781f837ef095c464d53e2d836acc6b0e79929aed74977490deaa8a362b67e
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data/CHANGELOG.md
CHANGED
data/README.md
CHANGED
@@ -62,7 +62,7 @@ ParseFasta::SeqFile.open(ARGV[0]).each_record do |rec|
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62
62
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# it's a fastQ record
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63
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else
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# it's a fastA record
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-
end
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65
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+
end
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end
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```
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68
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@@ -74,7 +74,7 @@ ParseFasta::SeqFile.open(ARGV[0]).each_record do |rec|
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# it's a fastQ record
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else
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# it's a fastA record
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77
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-
end
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77
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+
end
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78
78
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end
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79
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```
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80
80
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@@ -85,3 +85,11 @@ ParseFasta::SeqFile.open(ARGV[0]).each_record do |rec|
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85
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puts rec.to_s
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86
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end
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```
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88
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+
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89
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+
But of course, since it is a `#to_s` override...you don't even have to call it directly!
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+
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+
```ruby
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92
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+
ParseFasta::SeqFile.open(ARGV[0]).each_record do |rec|
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puts rec
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94
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+
end
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95
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+
```
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data/lib/parse_fasta/record.rb
CHANGED
@@ -52,9 +52,10 @@ module ParseFasta
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52
52
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@desc = args.fetch :desc, nil
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53
53
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@qual = args.fetch :qual, nil
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54
54
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|
55
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-
@qual.
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55
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+
@qual.tr!(" \t\n\r", "") if @qual
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56
56
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57
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-
seq = args.fetch(:seq)
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+
seq = args.fetch(:seq)
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58
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+
seq.tr!(" \t\n\r", "")
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58
59
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59
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if fastq? # is fastQ
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@seq = seq
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@@ -163,7 +164,7 @@ module ParseFasta
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163
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private
|
164
165
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165
166
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def check_fasta_seq seq
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166
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-
if seq.
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167
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+
if seq.include? ">"
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167
168
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raise ParseFasta::Error::SequenceFormatError,
|
168
169
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"A sequence contained a '>' character " +
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169
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"(the fastA file record separator)"
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data/lib/parse_fasta/version.rb
CHANGED
@@ -27,11 +27,11 @@ module ParseFasta
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27
27
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28
28
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let(:fasta_rec) {
|
29
29
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Record.new header: header,
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30
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-
seq: "A
|
30
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+
seq: "A \r\n\r\n\tC\t\t \n T G\r"
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31
31
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}
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32
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let(:fastq_rec) {
|
33
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Record.new header: header,
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-
seq: "A
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34
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+
seq: "A \r\n\r\n\tC\t\t \n T G\r",
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desc: desc,
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qual: " a b \tcd "
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}
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metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: parse_fasta
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 2.1.
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4
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+
version: 2.1.1
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5
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platform: ruby
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6
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authors:
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7
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- Ryan Moore
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8
8
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autorequire:
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9
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bindir: bin
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10
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cert_chain: []
|
11
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-
date: 2016-
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11
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+
date: 2016-11-01 00:00:00.000000000 Z
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12
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dependencies:
|
13
13
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- !ruby/object:Gem::Dependency
|
14
14
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name: bundler
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