crb-blast 0.3 → 0.3.1

Sign up to get free protection for your applications and to get access to all the features.
Files changed (3) hide show
  1. checksums.yaml +4 -4
  2. data/lib/crb-blast.rb +7 -0
  3. metadata +60 -30
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
1
1
  ---
2
2
  SHA1:
3
- metadata.gz: fb3b123812929285b57903de865b981104ffdfe9
4
- data.tar.gz: d66187a8a9b08b4bb282d03ed75898f1f5789af8
3
+ metadata.gz: 9f7c5625ff9b0713d25b0c8a4c28c56aa1316cb3
4
+ data.tar.gz: eaebeeedcfcc156bc7743a47683e8ce509abbe38
5
5
  SHA512:
6
- metadata.gz: 260463b1df616c63dbd262fb5d0e205610d221c4d81fdf0216e28fdcf8fde7d7f821c2e10d80edec969d5d9b64288823e169d06f7235abbca7553f1a633e9fd2
7
- data.tar.gz: cde2ffeb8b7efe84d6ca09f99358dc5dd7cf77f193dfc91669af7a9ba54e66712f085c9dbe26d45f7abe2e01a96f453568198b1516fedcecf2ee0f3cefcf6c70
6
+ metadata.gz: 6fc0fbe6d7f2399a68409e6211f013a457a95937665d6acd391d809df0c829583e6d7f5f1b6a12cf50aa6310731f1e206c5f25349100b1e295f37f1ea5a75baf
7
+ data.tar.gz: 8519e10ea5de7822542d0ce05d94dbe956e9151237b49bcab89bbab74d460acfa93f9beed8ce9dcf1816b5d49365d837daf87d48c998cfde4a14266053e2f142
data/lib/crb-blast.rb CHANGED
@@ -192,6 +192,9 @@ class CRB_Blast
192
192
  cat_cmd << blasts.join(" ")
193
193
  cat_cmd << " > #{@output1}"
194
194
  `#{cat_cmd}`
195
+ files.each do |file|
196
+ File.delete(file) if File.exist?(file)
197
+ end
195
198
  blasts.each do |b|
196
199
  File.delete(b) # delete intermediate blast output files
197
200
  end
@@ -213,6 +216,9 @@ class CRB_Blast
213
216
  cat_cmd << blasts.join(" ")
214
217
  cat_cmd << " > #{@output2}"
215
218
  `#{cat_cmd}`
219
+ files.each do |file|
220
+ File.delete(file) if File.exist?(file)
221
+ end
216
222
  blasts.each do |b|
217
223
  File.delete(b) # delete intermediate blast output files
218
224
  end
@@ -240,6 +246,7 @@ class CRB_Blast
240
246
  output_files=[]
241
247
  pieces.times do |n|
242
248
  outfile = "#{filename}_chunk_#{n}.fasta"
249
+ outfile = File.expand_path(outfile)
243
250
  outputs[n] = File.open("#{outfile}", "w")
244
251
  output_files[n] = "#{outfile}"
245
252
  end
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: crb-blast
3
3
  version: !ruby/object:Gem::Version
4
- version: '0.3'
4
+ version: 0.3.1
5
5
  platform: ruby
6
6
  authors:
7
7
  - Chris Boursnell
@@ -9,36 +9,22 @@ authors:
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2014-04-28 00:00:00.000000000 Z
12
+ date: 2014-07-18 00:00:00.000000000 Z
13
13
  dependencies:
14
14
  - !ruby/object:Gem::Dependency
15
15
  name: trollop
16
16
  requirement: !ruby/object:Gem::Requirement
17
17
  requirements:
18
- - - ">="
19
- - !ruby/object:Gem::Version
20
- version: '0'
21
- type: :runtime
22
- prerelease: false
23
- version_requirements: !ruby/object:Gem::Requirement
24
- requirements:
25
- - - ">="
26
- - !ruby/object:Gem::Version
27
- version: '0'
28
- - !ruby/object:Gem::Dependency
29
- name: rake
30
- requirement: !ruby/object:Gem::Requirement
31
- requirements:
32
- - - ">="
18
+ - - "~>"
33
19
  - !ruby/object:Gem::Version
34
- version: '0'
20
+ version: '2.0'
35
21
  type: :runtime
36
22
  prerelease: false
37
23
  version_requirements: !ruby/object:Gem::Requirement
38
24
  requirements:
39
- - - ">="
25
+ - - "~>"
40
26
  - !ruby/object:Gem::Version
41
- version: '0'
27
+ version: '2.0'
42
28
  - !ruby/object:Gem::Dependency
43
29
  name: bio
44
30
  requirement: !ruby/object:Gem::Requirement
@@ -78,6 +64,9 @@ dependencies:
78
64
  requirement: !ruby/object:Gem::Requirement
79
65
  requirements:
80
66
  - - "~>"
67
+ - !ruby/object:Gem::Version
68
+ version: '0.2'
69
+ - - ">="
81
70
  - !ruby/object:Gem::Version
82
71
  version: 0.2.0
83
72
  type: :runtime
@@ -85,6 +74,9 @@ dependencies:
85
74
  version_requirements: !ruby/object:Gem::Requirement
86
75
  requirements:
87
76
  - - "~>"
77
+ - !ruby/object:Gem::Version
78
+ version: '0.2'
79
+ - - ">="
88
80
  - !ruby/object:Gem::Version
89
81
  version: 0.2.0
90
82
  - !ruby/object:Gem::Dependency
@@ -107,62 +99,100 @@ dependencies:
107
99
  - - ">="
108
100
  - !ruby/object:Gem::Version
109
101
  version: 0.0.7
102
+ - !ruby/object:Gem::Dependency
103
+ name: rake
104
+ requirement: !ruby/object:Gem::Requirement
105
+ requirements:
106
+ - - "~>"
107
+ - !ruby/object:Gem::Version
108
+ version: '10.3'
109
+ - - ">="
110
+ - !ruby/object:Gem::Version
111
+ version: 10.3.2
112
+ type: :development
113
+ prerelease: false
114
+ version_requirements: !ruby/object:Gem::Requirement
115
+ requirements:
116
+ - - "~>"
117
+ - !ruby/object:Gem::Version
118
+ version: '10.3'
119
+ - - ">="
120
+ - !ruby/object:Gem::Version
121
+ version: 10.3.2
110
122
  - !ruby/object:Gem::Dependency
111
123
  name: turn
112
124
  requirement: !ruby/object:Gem::Requirement
113
125
  requirements:
126
+ - - "~>"
127
+ - !ruby/object:Gem::Version
128
+ version: '0.9'
114
129
  - - ">="
115
130
  - !ruby/object:Gem::Version
116
- version: '0'
131
+ version: 0.9.7
117
132
  type: :development
118
133
  prerelease: false
119
134
  version_requirements: !ruby/object:Gem::Requirement
120
135
  requirements:
136
+ - - "~>"
137
+ - !ruby/object:Gem::Version
138
+ version: '0.9'
121
139
  - - ">="
122
140
  - !ruby/object:Gem::Version
123
- version: '0'
141
+ version: 0.9.7
124
142
  - !ruby/object:Gem::Dependency
125
143
  name: simplecov
126
144
  requirement: !ruby/object:Gem::Requirement
127
145
  requirements:
146
+ - - "~>"
147
+ - !ruby/object:Gem::Version
148
+ version: '0.8'
128
149
  - - ">="
129
150
  - !ruby/object:Gem::Version
130
- version: '0'
151
+ version: 0.8.2
131
152
  type: :development
132
153
  prerelease: false
133
154
  version_requirements: !ruby/object:Gem::Requirement
134
155
  requirements:
156
+ - - "~>"
157
+ - !ruby/object:Gem::Version
158
+ version: '0.8'
135
159
  - - ">="
136
160
  - !ruby/object:Gem::Version
137
- version: '0'
161
+ version: 0.8.2
138
162
  - !ruby/object:Gem::Dependency
139
163
  name: shoulda-context
140
164
  requirement: !ruby/object:Gem::Requirement
141
165
  requirements:
166
+ - - "~>"
167
+ - !ruby/object:Gem::Version
168
+ version: '1.2'
142
169
  - - ">="
143
170
  - !ruby/object:Gem::Version
144
- version: '0'
171
+ version: 1.2.1
145
172
  type: :development
146
173
  prerelease: false
147
174
  version_requirements: !ruby/object:Gem::Requirement
148
175
  requirements:
176
+ - - "~>"
177
+ - !ruby/object:Gem::Version
178
+ version: '1.2'
149
179
  - - ">="
150
180
  - !ruby/object:Gem::Version
151
- version: '0'
181
+ version: 1.2.1
152
182
  - !ruby/object:Gem::Dependency
153
183
  name: coveralls
154
184
  requirement: !ruby/object:Gem::Requirement
155
185
  requirements:
156
- - - ">="
186
+ - - "~>"
157
187
  - !ruby/object:Gem::Version
158
- version: 0.6.7
188
+ version: '0.7'
159
189
  type: :development
160
190
  prerelease: false
161
191
  version_requirements: !ruby/object:Gem::Requirement
162
192
  requirements:
163
- - - ">="
193
+ - - "~>"
164
194
  - !ruby/object:Gem::Version
165
- version: 0.6.7
195
+ version: '0.7'
166
196
  description: See summary
167
197
  email: cmb211@cam.ac.uk
168
198
  executables: