parse_fasta 2.0.0 → 2.0.1
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- checksums.yaml +5 -13
- data/.travis.yml +2 -3
- data/lib/parse_fasta/seq_file.rb +34 -33
- data/lib/parse_fasta/version.rb +1 -1
- data/parse_fasta.gemspec +1 -1
- data/spec/test_files/test.rb +71 -0
- metadata +27 -25
checksums.yaml
CHANGED
@@ -1,15 +1,7 @@
|
|
1
1
|
---
|
2
|
-
|
3
|
-
metadata.gz:
|
4
|
-
|
5
|
-
data.tar.gz: !binary |-
|
6
|
-
OTgxOWFjYTEyMWI0MjNlNjBhZjJkNGZkMjFkZGFkZDNjNGJkNTk2NA==
|
2
|
+
SHA1:
|
3
|
+
metadata.gz: 9f779807eb98f39dfbbd67376e04a890be3a7bf9
|
4
|
+
data.tar.gz: 5f7201962d03a7c3b2553d576d4721822dbc24a2
|
7
5
|
SHA512:
|
8
|
-
metadata.gz:
|
9
|
-
|
10
|
-
NTI0NDk5NDY0NTc4YThhZTg4ODczYjAxZTA3MGNmZDdmMWYzNmMwMGFlMzhl
|
11
|
-
ODFhM2Q1NzIxZDVlYjE0MjEwYTg0OTlkMzlmZDQyYjIzYjhjNGQ=
|
12
|
-
data.tar.gz: !binary |-
|
13
|
-
MTBlN2NmNmJkOGUwM2Q1MDZhZTkzM2NmMzNmOTY1YWUzMzVjNjdkN2NiMDM2
|
14
|
-
NTJlYmU5Yzk1ODExNzczMGNkNTFkNzEwOWZkZGIwMjRiMjNiNGY5ZGM0MDJk
|
15
|
-
ZmY3YWI0OGQwOTNiMzY2ODAzMzkxZjFkZmNiNTExMGE3NWFlZjk=
|
6
|
+
metadata.gz: 9ddd0ae41bde830edba8af62be8ee88700e6c309b2f61ef0887a67579551d88308e0e53bbcb57c5d18ddd0cbc4b79f60a47986df14f2578415fa983ddbeb317f
|
7
|
+
data.tar.gz: ad89bb85f6cfcd8ed8af0d7c518d1b773cff2c9edcc5f51b241a149a55c217d070cbedca0946edb506b53ce430117d41ef7058a130e7e7e013dcc64c4d41b110
|
data/.travis.yml
CHANGED
data/lib/parse_fasta/seq_file.rb
CHANGED
@@ -18,39 +18,6 @@
|
|
18
18
|
|
19
19
|
require "zlib"
|
20
20
|
|
21
|
-
def get_first_char fname
|
22
|
-
if File.exists? fname
|
23
|
-
begin
|
24
|
-
f = Zlib::GzipReader.open fname
|
25
|
-
rescue Zlib::GzipFile::Error
|
26
|
-
f = File.open fname
|
27
|
-
ensure
|
28
|
-
# f.close
|
29
|
-
end
|
30
|
-
|
31
|
-
first_char = f.each_char.peek[0]
|
32
|
-
f.close
|
33
|
-
return first_char
|
34
|
-
else
|
35
|
-
raise ParseFasta::Error::FileNotFoundError,
|
36
|
-
"No such file or directory -- #{fname}"
|
37
|
-
end
|
38
|
-
end
|
39
|
-
|
40
|
-
def check_file fname
|
41
|
-
first_char = get_first_char fname
|
42
|
-
|
43
|
-
if first_char == ">"
|
44
|
-
:fasta
|
45
|
-
elsif first_char == "@"
|
46
|
-
:fastq
|
47
|
-
else
|
48
|
-
raise ParseFasta::Error::DataFormatError,
|
49
|
-
"The file does not look like fastA or fastQ " +
|
50
|
-
"-- #{fname}"
|
51
|
-
end
|
52
|
-
end
|
53
|
-
|
54
21
|
module ParseFasta
|
55
22
|
class SeqFile
|
56
23
|
# @!attribute type
|
@@ -250,5 +217,39 @@ module ParseFasta
|
|
250
217
|
|
251
218
|
line_reader
|
252
219
|
end
|
220
|
+
|
221
|
+
def get_first_char fname
|
222
|
+
if File.exists? fname
|
223
|
+
begin
|
224
|
+
f = Zlib::GzipReader.open fname
|
225
|
+
rescue Zlib::GzipFile::Error
|
226
|
+
f = File.open fname
|
227
|
+
end
|
228
|
+
|
229
|
+
begin
|
230
|
+
first_char = f.each_char.peek[0]
|
231
|
+
return first_char
|
232
|
+
ensure
|
233
|
+
f.close
|
234
|
+
end
|
235
|
+
else
|
236
|
+
raise ParseFasta::Error::FileNotFoundError,
|
237
|
+
"No such file or directory -- #{fname}"
|
238
|
+
end
|
239
|
+
end
|
240
|
+
|
241
|
+
def check_file fname
|
242
|
+
first_char = get_first_char fname
|
243
|
+
|
244
|
+
if first_char == ">"
|
245
|
+
:fasta
|
246
|
+
elsif first_char == "@"
|
247
|
+
:fastq
|
248
|
+
else
|
249
|
+
raise ParseFasta::Error::DataFormatError,
|
250
|
+
"The file does not look like fastA or fastQ " +
|
251
|
+
"-- #{fname}"
|
252
|
+
end
|
253
|
+
end
|
253
254
|
end
|
254
255
|
end
|
data/lib/parse_fasta/version.rb
CHANGED
data/parse_fasta.gemspec
CHANGED
@@ -21,7 +21,7 @@ Gem::Specification.new do |spec|
|
|
21
21
|
spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
|
22
22
|
spec.require_paths = ["lib"]
|
23
23
|
|
24
|
-
spec.required_ruby_version = ">=
|
24
|
+
spec.required_ruby_version = ">= 2"
|
25
25
|
|
26
26
|
spec.add_development_dependency "bundler", "~> 1.6"
|
27
27
|
spec.add_development_dependency "rake", "~> 10.3"
|
@@ -0,0 +1,71 @@
|
|
1
|
+
require "parse_fasta"
|
2
|
+
|
3
|
+
fasta_records =
|
4
|
+
[ParseFasta::Record.new(header: "empty seq at beginning",
|
5
|
+
seq: ""),
|
6
|
+
ParseFasta::Record.new(header: "seq1 is fun",
|
7
|
+
seq: "AACTGGNNN"),
|
8
|
+
ParseFasta::Record.new(header: "seq2",
|
9
|
+
seq: "AATCCTGNNN"),
|
10
|
+
ParseFasta::Record.new(header: "empty seq 1",
|
11
|
+
seq: ""),
|
12
|
+
ParseFasta::Record.new(header: "empty seq 2",
|
13
|
+
seq: ""),
|
14
|
+
ParseFasta::Record.new(header: "seq3",
|
15
|
+
seq: "yyyyyyyyyyyyyyyNNN"),
|
16
|
+
ParseFasta::Record.new(header: "seq 4 > has many '>' in header",
|
17
|
+
seq: "ACTGactg"),
|
18
|
+
ParseFasta::Record.new(header: "empty seq at end",
|
19
|
+
seq: "")]
|
20
|
+
|
21
|
+
fastq_records =
|
22
|
+
[ParseFasta::Record.new(header: "seq1",
|
23
|
+
seq: "AA CC TT GG",
|
24
|
+
desc: "",
|
25
|
+
qual: ")# 3g Tq N8"),
|
26
|
+
ParseFasta::Record.new(header: "seq2 @pples",
|
27
|
+
seq: "ACTG",
|
28
|
+
desc: "seq2 +pples",
|
29
|
+
qual: "*ujM")]
|
30
|
+
|
31
|
+
|
32
|
+
line_endings_fastq_records =
|
33
|
+
[ParseFasta::Record.new(header: "apple", seq: "ACTG", desc: "", qual: "IIII"),
|
34
|
+
ParseFasta::Record.new(header: "pie", seq: "AACC", desc: "", qual: "BBBB"),]
|
35
|
+
|
36
|
+
line_endings_fasta_records =
|
37
|
+
[ParseFasta::Record.new(header: "apple", seq: "ACTG"),
|
38
|
+
ParseFasta::Record.new(header: "pie", seq: "AACC"),]
|
39
|
+
|
40
|
+
def check fname, expected_records
|
41
|
+
STDERR.puts "\nReading #{fname}"
|
42
|
+
recs = []
|
43
|
+
ParseFasta::SeqFile.open(File.join File.dirname(__FILE__), fname).each_record do |rec|
|
44
|
+
p [rec.header, rec.seq, rec.desc, rec.qual]
|
45
|
+
recs << rec
|
46
|
+
end
|
47
|
+
STDERR.puts "Good? #{recs == expected_records}"
|
48
|
+
|
49
|
+
$results << (recs == expected_records)
|
50
|
+
end
|
51
|
+
|
52
|
+
$results = []
|
53
|
+
|
54
|
+
check "seqs.fa", fasta_records
|
55
|
+
check "seqs.fa.gz", fasta_records
|
56
|
+
check "seqs.fq", fastq_records
|
57
|
+
check "seqs.fq.gz", fastq_records
|
58
|
+
|
59
|
+
check "cr.fa", line_endings_fasta_records
|
60
|
+
check "cr.fa.gz", line_endings_fasta_records
|
61
|
+
check "cr_nl.fa", line_endings_fasta_records
|
62
|
+
check "cr_nl.fa.gz", line_endings_fasta_records
|
63
|
+
|
64
|
+
check "cr.fq", line_endings_fastq_records
|
65
|
+
check "cr.fq.gz", line_endings_fastq_records
|
66
|
+
check "cr_nl.fq", line_endings_fastq_records
|
67
|
+
check "cr_nl.fq.gz", line_endings_fastq_records
|
68
|
+
|
69
|
+
if $results.all? { |res| res }
|
70
|
+
STDERR.puts "\nAll Good!\n\n"
|
71
|
+
end
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: parse_fasta
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 2.0.
|
4
|
+
version: 2.0.1
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Ryan Moore
|
@@ -14,98 +14,98 @@ dependencies:
|
|
14
14
|
name: bundler
|
15
15
|
requirement: !ruby/object:Gem::Requirement
|
16
16
|
requirements:
|
17
|
-
- - ~>
|
17
|
+
- - "~>"
|
18
18
|
- !ruby/object:Gem::Version
|
19
19
|
version: '1.6'
|
20
20
|
type: :development
|
21
21
|
prerelease: false
|
22
22
|
version_requirements: !ruby/object:Gem::Requirement
|
23
23
|
requirements:
|
24
|
-
- - ~>
|
24
|
+
- - "~>"
|
25
25
|
- !ruby/object:Gem::Version
|
26
26
|
version: '1.6'
|
27
27
|
- !ruby/object:Gem::Dependency
|
28
28
|
name: rake
|
29
29
|
requirement: !ruby/object:Gem::Requirement
|
30
30
|
requirements:
|
31
|
-
- - ~>
|
31
|
+
- - "~>"
|
32
32
|
- !ruby/object:Gem::Version
|
33
33
|
version: '10.3'
|
34
34
|
type: :development
|
35
35
|
prerelease: false
|
36
36
|
version_requirements: !ruby/object:Gem::Requirement
|
37
37
|
requirements:
|
38
|
-
- - ~>
|
38
|
+
- - "~>"
|
39
39
|
- !ruby/object:Gem::Version
|
40
40
|
version: '10.3'
|
41
41
|
- !ruby/object:Gem::Dependency
|
42
42
|
name: rspec
|
43
43
|
requirement: !ruby/object:Gem::Requirement
|
44
44
|
requirements:
|
45
|
-
- - ~>
|
45
|
+
- - "~>"
|
46
46
|
- !ruby/object:Gem::Version
|
47
47
|
version: '2.14'
|
48
48
|
type: :development
|
49
49
|
prerelease: false
|
50
50
|
version_requirements: !ruby/object:Gem::Requirement
|
51
51
|
requirements:
|
52
|
-
- - ~>
|
52
|
+
- - "~>"
|
53
53
|
- !ruby/object:Gem::Version
|
54
54
|
version: '2.14'
|
55
55
|
- !ruby/object:Gem::Dependency
|
56
56
|
name: bio
|
57
57
|
requirement: !ruby/object:Gem::Requirement
|
58
58
|
requirements:
|
59
|
-
- - ~>
|
59
|
+
- - "~>"
|
60
60
|
- !ruby/object:Gem::Version
|
61
61
|
version: '1.4'
|
62
62
|
type: :development
|
63
63
|
prerelease: false
|
64
64
|
version_requirements: !ruby/object:Gem::Requirement
|
65
65
|
requirements:
|
66
|
-
- - ~>
|
66
|
+
- - "~>"
|
67
67
|
- !ruby/object:Gem::Version
|
68
68
|
version: '1.4'
|
69
69
|
- !ruby/object:Gem::Dependency
|
70
70
|
name: yard
|
71
71
|
requirement: !ruby/object:Gem::Requirement
|
72
72
|
requirements:
|
73
|
-
- - ~>
|
73
|
+
- - "~>"
|
74
74
|
- !ruby/object:Gem::Version
|
75
75
|
version: '0.8'
|
76
76
|
type: :development
|
77
77
|
prerelease: false
|
78
78
|
version_requirements: !ruby/object:Gem::Requirement
|
79
79
|
requirements:
|
80
|
-
- - ~>
|
80
|
+
- - "~>"
|
81
81
|
- !ruby/object:Gem::Version
|
82
82
|
version: '0.8'
|
83
83
|
- !ruby/object:Gem::Dependency
|
84
84
|
name: rdiscount
|
85
85
|
requirement: !ruby/object:Gem::Requirement
|
86
86
|
requirements:
|
87
|
-
- -
|
87
|
+
- - ">="
|
88
88
|
- !ruby/object:Gem::Version
|
89
89
|
version: '0'
|
90
90
|
type: :development
|
91
91
|
prerelease: false
|
92
92
|
version_requirements: !ruby/object:Gem::Requirement
|
93
93
|
requirements:
|
94
|
-
- -
|
94
|
+
- - ">="
|
95
95
|
- !ruby/object:Gem::Version
|
96
96
|
version: '0'
|
97
97
|
- !ruby/object:Gem::Dependency
|
98
98
|
name: coveralls
|
99
99
|
requirement: !ruby/object:Gem::Requirement
|
100
100
|
requirements:
|
101
|
-
- - ~>
|
101
|
+
- - "~>"
|
102
102
|
- !ruby/object:Gem::Version
|
103
103
|
version: '0.7'
|
104
104
|
type: :development
|
105
105
|
prerelease: false
|
106
106
|
version_requirements: !ruby/object:Gem::Requirement
|
107
107
|
requirements:
|
108
|
-
- - ~>
|
108
|
+
- - "~>"
|
109
109
|
- !ruby/object:Gem::Version
|
110
110
|
version: '0.7'
|
111
111
|
description: Provides nice, programmatic access to fasta and fastq files, as well
|
@@ -118,11 +118,11 @@ executables:
|
|
118
118
|
extensions: []
|
119
119
|
extra_rdoc_files: []
|
120
120
|
files:
|
121
|
-
- .coveralls.yml
|
122
|
-
- .gitignore
|
123
|
-
- .rspec
|
124
|
-
- .travis.yml
|
125
|
-
- .yardopts
|
121
|
+
- ".coveralls.yml"
|
122
|
+
- ".gitignore"
|
123
|
+
- ".rspec"
|
124
|
+
- ".travis.yml"
|
125
|
+
- ".yardopts"
|
126
126
|
- CHANGELOG.md
|
127
127
|
- COPYING
|
128
128
|
- Gemfile
|
@@ -156,9 +156,10 @@ files:
|
|
156
156
|
- spec/test_files/seqs.fa.gz
|
157
157
|
- spec/test_files/seqs.fq
|
158
158
|
- spec/test_files/seqs.fq.gz
|
159
|
+
- spec/test_files/test.rb
|
159
160
|
homepage: https://github.com/mooreryan/parse_fasta
|
160
161
|
licenses:
|
161
|
-
-
|
162
|
+
- 'GPLv3: http://www.gnu.org/licenses/gpl.txt'
|
162
163
|
metadata: {}
|
163
164
|
post_install_message:
|
164
165
|
rdoc_options: []
|
@@ -166,17 +167,17 @@ require_paths:
|
|
166
167
|
- lib
|
167
168
|
required_ruby_version: !ruby/object:Gem::Requirement
|
168
169
|
requirements:
|
169
|
-
- -
|
170
|
+
- - ">="
|
170
171
|
- !ruby/object:Gem::Version
|
171
|
-
version:
|
172
|
+
version: '2'
|
172
173
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
173
174
|
requirements:
|
174
|
-
- -
|
175
|
+
- - ">="
|
175
176
|
- !ruby/object:Gem::Version
|
176
177
|
version: '0'
|
177
178
|
requirements: []
|
178
179
|
rubyforge_project:
|
179
|
-
rubygems_version: 2.
|
180
|
+
rubygems_version: 2.5.1
|
180
181
|
signing_key:
|
181
182
|
specification_version: 4
|
182
183
|
summary: Easy-peasy parsing of fasta & fastq files!
|
@@ -201,4 +202,5 @@ test_files:
|
|
201
202
|
- spec/test_files/seqs.fa.gz
|
202
203
|
- spec/test_files/seqs.fq
|
203
204
|
- spec/test_files/seqs.fq.gz
|
205
|
+
- spec/test_files/test.rb
|
204
206
|
has_rdoc:
|