bio-polyploid-tools 0.4.3 → 0.4.4
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/bio-polyploid-tools.gemspec +2 -2
- data/lib/bio/PolyploidTools/ExonContainer.rb +1 -1
- data/lib/bio/db/primer3.rb +9 -4
- metadata +1 -1
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: c65f3649faacf8bbf2fdb2269a6ed125841ba74c
|
4
|
+
data.tar.gz: a3ef8e79ccc3feeaece52dca1dafdd1bf74888cd
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 0fe43f7748842d15ac6e08feab09c7fba77b7fe9b7879a091df5c622cca453f5d7878c6ae39447dc4bb26ca4239d4a80700d69a84fb20348d7891d7be68d689a
|
7
|
+
data.tar.gz: 257ec9bc355fa195148b67600d0507edaff4b5144c1a05db4b95ac468bede2ca09dab8b459dd2131d0f98a23018bf777d6fe8e819084bc173049c8d4e0ab8878
|
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
|
-
0.4.
|
1
|
+
0.4.4
|
data/bio-polyploid-tools.gemspec
CHANGED
@@ -2,11 +2,11 @@
|
|
2
2
|
# DO NOT EDIT THIS FILE DIRECTLY
|
3
3
|
# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
|
4
4
|
# -*- encoding: utf-8 -*-
|
5
|
-
# stub: bio-polyploid-tools 0.4.
|
5
|
+
# stub: bio-polyploid-tools 0.4.4 ruby lib
|
6
6
|
|
7
7
|
Gem::Specification.new do |s|
|
8
8
|
s.name = "bio-polyploid-tools"
|
9
|
-
s.version = "0.4.
|
9
|
+
s.version = "0.4.4"
|
10
10
|
|
11
11
|
s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
12
12
|
s.require_paths = ["lib"]
|
data/lib/bio/db/primer3.rb
CHANGED
@@ -1,4 +1,4 @@
|
|
1
|
-
|
1
|
+
require 'pp'
|
2
2
|
module Bio::DB::Primer3
|
3
3
|
class Primer3Exception < RuntimeError
|
4
4
|
end
|
@@ -158,12 +158,16 @@ module Bio::DB::Primer3
|
|
158
158
|
values << "second"
|
159
159
|
values << primer3_line_2.shortest_pair.product_size
|
160
160
|
else
|
161
|
+
|
161
162
|
first_candidate = find_primer_pair_first
|
162
163
|
second_candidate = find_primer_pair_second
|
163
164
|
|
164
165
|
if first_candidate
|
166
|
+
|
167
|
+
#puts "input to search #{first_candidate.left_coordinates}"
|
165
168
|
primer_2 = primer3_line_2.left_primer_with_coordinates(first_candidate.left_coordinates, first_candidate.orientation)
|
166
169
|
primer_2_tm = find_left_primer_temp(primer_2)
|
170
|
+
#puts "In the funky if #{primer_2}"
|
167
171
|
end
|
168
172
|
if second_candidate
|
169
173
|
primer_1 = primer3_line_1.left_primer_with_coordinates(second_candidate.left_coordinates, second_candidate.orientation)
|
@@ -283,7 +287,7 @@ module Bio::DB::Primer3
|
|
283
287
|
primers_line_1 << primer3record
|
284
288
|
@primer3_line_1 = primer3record if not @primer3_line_1 or @primer3_line_1 > primer3record
|
285
289
|
when primer3record.line == @line_2
|
286
|
-
|
290
|
+
primers_line_2 << primer3record
|
287
291
|
@primer3_line_2 = primer3record if not @primer3_line_2 or @primer3_line_2 > primer3record
|
288
292
|
else
|
289
293
|
raise Primer3Exception.new "#{primer3record.line} is not recognized (#{line_1}, #{line_2})"
|
@@ -419,13 +423,14 @@ module Bio::DB::Primer3
|
|
419
423
|
else
|
420
424
|
raise Primer3Exception.new "#{tmp_primer} doesnt end in a base in the SNP #{snp.to_s}"
|
421
425
|
end
|
426
|
+
#puts "tmp_primer: #{tmp_primer}"
|
422
427
|
return tmp_primer
|
423
428
|
end
|
424
429
|
|
425
430
|
def left_primer_with_coordinates(coordinates, other_orientation)
|
426
431
|
|
427
432
|
seq = self.sequence_template
|
428
|
-
|
433
|
+
#puts "Left coordinates: #{seq}"
|
429
434
|
seq = reverse_complement_string(seq) if self.orientation != other_orientation
|
430
435
|
|
431
436
|
seq[coordinates[0],coordinates[1]]
|
@@ -687,7 +692,7 @@ module Bio::DB::Primer3
|
|
687
692
|
Primer3Record.parse_file(filename) do | primer3record |
|
688
693
|
current_snp = @snp_hash["#{primer3record.snp.to_s}:#{primer3record.chromosome}"]
|
689
694
|
current_snp.add_record(primer3record)
|
690
|
-
|
695
|
+
|
691
696
|
end
|
692
697
|
end
|
693
698
|
|