scbi_fasta 0.1.8 → 0.1.9
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- data/History.txt +4 -0
- data/lib/scbi_fasta.rb +1 -1
- data/lib/scbi_fasta/fasta_qual_file.rb +17 -12
- data/test/test_fasta_qual_file.rb +26 -25
- metadata +2 -2
data/History.txt
CHANGED
data/lib/scbi_fasta.rb
CHANGED
@@ -34,11 +34,12 @@ attr_accessor :num_seqs, :end_fasta
|
|
34
34
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@with_qual = false
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35
35
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#raise "File #{qual_file_name} doesn't exists"
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36
36
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end
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37
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-
|
37
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+
# puts "With_qual #{fasta_file_name}?: #{@with_qual}"
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38
38
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39
39
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@num_seqs = 0 ;
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40
40
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41
41
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@seq_name = '';
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42
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+
@seq_comment='';
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42
43
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@file_fasta = File.open(fasta_file_name) ;
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43
44
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@end_fasta=false;
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44
45
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@@ -67,16 +68,17 @@ attr_accessor :num_seqs, :end_fasta
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67
68
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68
69
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rewind
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69
70
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|
70
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-
n,f,q=next_seq
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71
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+
n,f,q,c = next_seq
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71
72
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while (!n.nil?)
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72
73
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73
74
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if @with_qual
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74
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-
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75
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+
|
76
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+
yield(n,f,q,c)
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75
77
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else
|
76
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-
yield(n,f)
|
78
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+
yield(n,f,q)
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77
79
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end
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78
80
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|
79
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-
n,f,q=next_seq
|
81
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+
n,f,q,c=next_seq
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80
82
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end
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81
83
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82
84
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rewind
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@@ -89,6 +91,7 @@ attr_accessor :num_seqs, :end_fasta
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89
91
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@num_seqs = 0 ;
|
90
92
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|
91
93
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@seq_name = '';
|
94
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+
@seq_comment= '';
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92
95
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@file_fasta.pos=0
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93
96
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@end_fasta=false;
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94
97
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@@ -111,7 +114,7 @@ attr_accessor :num_seqs, :end_fasta
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|
111
114
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# envia on_process_sequence
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112
115
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if ((!@end_fasta) && (!@with_qual or !@end_qual))
|
113
116
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|
114
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-
name_f,fasta=read_fasta
|
117
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+
name_f,fasta,comment=read_fasta
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115
118
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116
119
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if @with_qual
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117
120
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@@ -129,9 +132,9 @@ attr_accessor :num_seqs, :end_fasta
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129
132
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if fasta.length == qual.count(' ') + 1
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130
133
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if @qual_to_array
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131
134
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a_qual = qual.strip.split(/\s/).map{|e| e.to_i}
|
132
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-
res =[name_f,fasta,a_qual]
|
135
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+
res =[name_f,fasta,a_qual,comment]
|
133
136
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else
|
134
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-
res =[name_f,fasta,qual]
|
137
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+
res =[name_f,fasta,qual,comment]
|
135
138
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end
|
136
139
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|
137
140
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else #if (!a_qual.empty?)
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@@ -141,7 +144,7 @@ attr_accessor :num_seqs, :end_fasta
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|
141
144
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end
|
142
145
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|
143
146
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else # without qual
|
144
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-
res =[name_f,fasta]
|
147
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+
res =[name_f,fasta,comment]
|
145
148
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end
|
146
149
|
end
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147
150
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@@ -179,17 +182,19 @@ attr_accessor :num_seqs, :end_fasta
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|
179
182
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if !@seq_name.empty?
|
180
183
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# ya había leido una
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181
184
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#puts "leida #{@seq_name} + #{@seq_fasta}"
|
182
|
-
res = [@seq_name,seq_fasta]
|
185
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+
res = [@seq_name,seq_fasta, @seq_comment]
|
183
186
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end
|
184
187
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|
185
188
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|
186
189
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#get only name
|
187
190
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line_fasta.gsub!(/^>\s*/,'');
|
188
191
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|
189
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-
line_fasta =~ /(^[^\s]+)/
|
192
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+
# line_fasta =~ /(^[^\s]+)/
|
193
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+
line_fasta =~ /(^[^\s]+)\s*(.*)$/
|
190
194
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# remove comments
|
191
195
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|
192
196
|
@seq_name = $1
|
197
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+
@seq_comment = $2
|
193
198
|
|
194
199
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seq_fasta='';
|
195
200
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|
@@ -211,7 +216,7 @@ attr_accessor :num_seqs, :end_fasta
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|
211
216
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|
212
217
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#si no hay más secuencias hay que devolver la última, CASO EOF
|
213
218
|
if res.nil? and !@seq_name.empty?
|
214
|
-
res= [@seq_name,seq_fasta]
|
219
|
+
res= [@seq_name,seq_fasta, @seq_comment]
|
215
220
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end
|
216
221
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|
217
222
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return res
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@@ -4,7 +4,7 @@ class TestFastaQualFile < Test::Unit::TestCase
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4
4
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|
5
5
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|
6
6
|
def setup
|
7
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-
@test_file='/tmp/
|
7
|
+
@test_file='/tmp/scbi_fasta';
|
8
8
|
|
9
9
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@seq_fasta='ACTG'
|
10
10
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@seq_qual=[25]
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@@ -19,7 +19,7 @@ class TestFastaQualFile < Test::Unit::TestCase
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19
19
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|
20
20
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n.times do |c|
|
21
21
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i = c+1
|
22
|
-
name = ">#{@seq_name+i.to_s} comments"
|
22
|
+
name = ">#{@seq_name+i.to_s} comments#{i}"
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23
23
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|
24
24
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f.puts(name)
|
25
25
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f.puts(@seq_fasta*i)
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@@ -46,13 +46,13 @@ class TestFastaQualFile < Test::Unit::TestCase
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46
46
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|
47
47
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100.times do |c|
|
48
48
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i = c+1
|
49
|
-
n,s,q = fqr.next_seq
|
49
|
+
n,s,q,c = fqr.next_seq
|
50
50
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|
51
51
|
#puts n,s.length,q.split(' ').length
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52
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-
|
53
|
-
|
54
|
-
|
55
|
-
|
52
|
+
assert_equal(@seq_name+i.to_s,n)
|
53
|
+
assert_equal(@seq_fasta*i,s)
|
54
|
+
assert_equal((@seq_qual*i*@seq_fasta.length).join(' '),q)
|
55
|
+
assert_equal('comments'+i.to_s,c)
|
56
56
|
end
|
57
57
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|
58
58
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fqr.close
|
@@ -74,13 +74,13 @@ class TestFastaQualFile < Test::Unit::TestCase
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|
74
74
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|
75
75
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i=1
|
76
76
|
|
77
|
-
fqr.each do |n,s,q|
|
77
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+
fqr.each do |n,s,q,c|
|
78
78
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|
79
79
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#puts n,s.length,q.split(' ').length
|
80
|
-
|
81
|
-
|
82
|
-
|
83
|
-
|
80
|
+
assert_equal(@seq_name+i.to_s,n)
|
81
|
+
assert_equal(@seq_fasta*i,s)
|
82
|
+
assert_equal((@seq_qual*i*@seq_fasta.length).join(' '),q)
|
83
|
+
assert_equal('comments'+i.to_s,c)
|
84
84
|
i+=1
|
85
85
|
end
|
86
86
|
|
@@ -105,11 +105,12 @@ class TestFastaQualFile < Test::Unit::TestCase
|
|
105
105
|
|
106
106
|
100.times do |c|
|
107
107
|
i = c+1
|
108
|
-
n,s,q = fqr.next_seq
|
108
|
+
n,s,c,q = fqr.next_seq
|
109
109
|
|
110
|
-
#puts n,s.length,q.split(' ').length
|
111
|
-
|
112
|
-
|
110
|
+
# puts n,s.length,q.split(' ').length
|
111
|
+
assert_equal(@seq_name+i.to_s,n)
|
112
|
+
assert_equal(@seq_fasta*i,s)
|
113
|
+
assert_equal('comments'+i.to_s,c)
|
113
114
|
assert(q.nil?)
|
114
115
|
|
115
116
|
end
|
@@ -135,12 +136,12 @@ class TestFastaQualFile < Test::Unit::TestCase
|
|
135
136
|
|
136
137
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i=1
|
137
138
|
|
138
|
-
fqr.each do |n,s,q|
|
139
|
-
|
139
|
+
fqr.each do |n,s,c,q|
|
140
|
+
# puts n,s,q
|
140
141
|
#puts n,s.length,q.split(' ').length
|
141
|
-
|
142
|
-
|
143
|
-
|
142
|
+
assert_equal(@seq_name+i.to_s,n)
|
143
|
+
assert_equal(@seq_fasta*i,s)
|
144
|
+
assert_equal('comments'+i.to_s,c)
|
144
145
|
assert(q.nil?)
|
145
146
|
|
146
147
|
i+=1
|
@@ -150,10 +151,10 @@ class TestFastaQualFile < Test::Unit::TestCase
|
|
150
151
|
|
151
152
|
fqr.close
|
152
153
|
|
153
|
-
rescue Exception => e
|
154
|
-
|
155
|
-
|
156
|
-
|
154
|
+
# rescue Exception => e
|
155
|
+
# puts "failed in #{n} , #{s}"
|
156
|
+
# puts "expected #{@seq_name+i.to_s} , #{@seq_fasta*i==s}"
|
157
|
+
# puts e.message, e.backtrace
|
157
158
|
|
158
159
|
end
|
159
160
|
|
metadata
CHANGED
@@ -2,7 +2,7 @@
|
|
2
2
|
name: scbi_fasta
|
3
3
|
version: !ruby/object:Gem::Version
|
4
4
|
prerelease:
|
5
|
-
version: 0.1.
|
5
|
+
version: 0.1.9
|
6
6
|
platform: ruby
|
7
7
|
authors:
|
8
8
|
- Almudena Bocinos
|
@@ -10,7 +10,7 @@ autorequire:
|
|
10
10
|
bindir: bin
|
11
11
|
cert_chain: []
|
12
12
|
|
13
|
-
date: 2011-
|
13
|
+
date: 2011-10-28 00:00:00 Z
|
14
14
|
dependencies:
|
15
15
|
- !ruby/object:Gem::Dependency
|
16
16
|
name: hoe
|