seqtrimnext 2.0.33 → 2.0.35
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- data/History.txt +8 -0
- data/bin/create_graphs.rb +6 -4
- data/lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb +19 -16
- data/lib/seqtrimnext/classes/params.rb +26 -11
- data/lib/seqtrimnext/classes/seqtrim.rb +1 -0
- data/lib/seqtrimnext/plugins/plugin.rb +1 -1
- data/lib/seqtrimnext/plugins/plugin_ab_adapters.rb +19 -1
- data/lib/seqtrimnext.rb +1 -1
- metadata +2 -2
data/History.txt
CHANGED
data/bin/create_graphs.rb
CHANGED
@@ -1,14 +1,16 @@
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1
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+
#!/usr/bin/env ruby
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2
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require 'stringio'
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3
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# require 'test/unit'
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4
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+
require 'seqtrimnext'
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5
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require 'json'
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6
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require 'gnuplot'
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5
7
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6
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-
ROOT_PATH=File.dirname(File.dirname(__FILE__))
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8
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+
# ROOT_PATH=File.dirname(File.dirname(__FILE__))
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9
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8
10
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# $: << File.expand_path(File.join(ROOT_PATH,'test'))
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9
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-
$: << File.expand_path(File.join(ROOT_PATH,'classes'))
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10
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-
$: << File.expand_path(File.join(ROOT_PATH,'plugins'))
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11
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-
$: << File.expand_path(File.join(ROOT_PATH,'utils'))
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11
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+
# $: << File.expand_path(File.join(ROOT_PATH,'classes'))
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12
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+
# $: << File.expand_path(File.join(ROOT_PATH,'plugins'))
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13
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+
# $: << File.expand_path(File.join(ROOT_PATH,'utils'))
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14
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13
15
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if ARGV.empty?
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16
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puts "Usage: #{$0} stats.json initial_stats.json"
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@@ -1,26 +1,29 @@
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1
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2
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#finds the classes that were in the folder 'classes'
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3
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4
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-
ROOT_PATH=File.dirname(File.dirname(File.dirname(__FILE__)))
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-
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6
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-
$: << File.expand_path(File.join(ROOT_PATH, 'classes'))
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7
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-
$: << File.expand_path(File.join(ROOT_PATH, 'classes','blast'))
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-
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9
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-
#finds the classes that were in the folder 'plugins'
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10
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-
$: << File.expand_path(File.join(ROOT_PATH, 'plugins'))
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11
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-
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12
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-
#finds the classes that were in the folder 'plugins'
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13
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-
$: << File.expand_path(File.join(ROOT_PATH, 'actions'))
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14
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-
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15
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-
#finds the classes that were in the folder 'utils'
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16
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-
$: << File.expand_path(File.join(ROOT_PATH, 'utils'))
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17
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-
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18
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-
$: << File.expand_path(File.join(ROOT_PATH, 'classes','em_classes'))
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4
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+
# ROOT_PATH=File.dirname(File.dirname(File.dirname(__FILE__)))
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#
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# $: << File.expand_path(File.join(ROOT_PATH, 'classes'))
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+
# $: << File.expand_path(File.join(ROOT_PATH, 'classes','blast'))
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+
#
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9
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# #finds the classes that were in the folder 'plugins'
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10
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# $: << File.expand_path(File.join(ROOT_PATH, 'plugins'))
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11
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+
#
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12
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+
# #finds the classes that were in the folder 'plugins'
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13
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+
# $: << File.expand_path(File.join(ROOT_PATH, 'actions'))
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14
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+
#
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15
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+
# #finds the classes that were in the folder 'utils'
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16
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# $: << File.expand_path(File.join(ROOT_PATH, 'utils'))
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17
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+
#
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18
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+
# $: << File.expand_path(File.join(ROOT_PATH, 'classes','em_classes'))
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19
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#
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20
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+
# $: << File.expand_path(ROOT_PATH)
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19
21
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20
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-
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22
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+
require 'seqtrimnext'
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$SEQTRIM_PATH = ROOT_PATH
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25
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26
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+
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if ENV['BLASTDB']# && Dir.exists?(ENV['BLASTDB'])
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$FORMATTED_DB_PATH = ENV['BLASTDB']
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$DB_PATH = File.dirname($FORMATTED_DB_PATH)
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@@ -12,6 +12,7 @@ class Params
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12
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@comments = {}
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13
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# @param_order={}
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14
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@mids = {}
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15
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+
@ab_adapters={}
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@linkers = {}
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@clusters = {}
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18
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@@ -54,28 +55,36 @@ class Params
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end
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56
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end# end def
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57
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57
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-
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58
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-
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58
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+
def load_db_fastas(path_file)
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59
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+
res={}
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60
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if File.exists?(path_file)
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61
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ff = FastaFile.new(path_file)
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ff.each {|n,f|
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# @mid_sizes[n]=f.size
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63
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-
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64
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+
res[n]=f
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}
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66
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66
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ff.close
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end
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+
return res
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end
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71
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+
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72
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# Load mid's file
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73
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def load_mids(path_file)
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74
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@mids=load_db_fastas(path_file)
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75
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# puts @mids
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76
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end
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77
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+
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78
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# Load ab_adapters file
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79
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def load_ab_adapters(path_file)
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80
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@ab_adapters=load_db_fastas(path_file)
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# puts @ab_adapters
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68
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end
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83
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70
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# Load mid's file
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71
85
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def load_linkers(path_file)
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72
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-
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73
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-
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74
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-
ff.each {|n,f|
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75
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-
@linkers[n]=f
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76
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-
}
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77
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-
ff.close
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78
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-
end
|
86
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+
@linkers=load_db_fastas(path_file)
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87
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# puts @linkers
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end
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89
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81
90
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def load_repeated_seqs(file_path)
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@@ -90,7 +99,7 @@ class Params
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90
99
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#if (line[0]!=62) && (line[0]!=48)
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91
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if (line[0]!='>'[0]) && (line[0]!='0'[0])
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101
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#puts line
|
93
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-
#puts line,line[0]
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102
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+
# puts line,line[0]
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94
103
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if line =~ />([^\.]+)\.\.\.\s/
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95
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#puts 'ok'
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@clusters[$1]=1
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@@ -157,6 +166,12 @@ class Params
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157
166
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return @linkers[linker]
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158
167
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end
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159
168
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|
169
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+
# Return the ab of param
|
170
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+
def get_ab_adapter(adapter)
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171
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return @ab_adapters[adapter]
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172
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end
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173
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+
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174
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+
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160
175
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def get_plugin
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plugin='General'
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177
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# puts caller(2)[1]
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@@ -223,6 +223,7 @@ class Seqtrim
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223
223
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224
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# leer mids
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225
225
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params.load_mids(File.join($FORMATTED_DB_PATH,'mids.fasta'))
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226
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+
params.load_ab_adapters(File.join($FORMATTED_DB_PATH,'adapters_ab.fasta'))
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227
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params.load_linkers(File.join($FORMATTED_DB_PATH,'linkers.fasta'))
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227
228
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228
229
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@@ -66,7 +66,7 @@ class Plugin
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# puts r2_end.class
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# puts "-------"
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#puts "overlap? (#{r1_start}<=#{r2_end}) and (#{r1_end}>=#{r2_start})"
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69
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-
return ((r1_start<=r2_end) and (r1_end>=r2_start) )
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+
return ((r1_start<=r2_end+1) and (r1_end>=r2_start-1) )
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end
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71
71
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|
72
72
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def merge_hits(hits,merged_hits,merged_ids=nil)
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@@ -43,6 +43,18 @@ class PluginAbAdapters < Plugin
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43
43
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return blast_table_results
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44
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end
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45
45
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|
46
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+
# filter hits that are far the extreme and do not have a valid length
|
47
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+
def filter_hits(hits,end_pos)
|
48
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hits.reverse_each do |hit|
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49
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if (hit.q_end < (end_pos-40)) && ((hit.q_end-hit.q_beg+1)<(@params.get_ab_adapter(hit.subject_id).length*0.80).to_i)
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hits.delete(hit)
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51
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# puts "DELETE #{hit.inspect}"
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# else
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# puts "ACCEPTED #{hit.inspect}, >= #{(@params.get_ab_adapter(hit.subject_id).length*0.2).to_i}"
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end
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end
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+
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end
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46
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def exec_seq(seq,blast_query)
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48
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if blast_query.query_id != seq.seq_name
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@@ -62,8 +74,10 @@ class PluginAbAdapters < Plugin
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62
74
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# blast_table_results = blast.do_blast(seq.seq_fasta) #rise seq to adapterss executing over blast
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#BlastTableResult.new(res)
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-
# puts
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# puts blast_query.inspect
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78
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# puts blast_table_results.inspect
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79
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+
|
80
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filter_hits(blast_query.hits, seq.seq_fasta.length)
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67
81
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68
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adapters=[]
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# blast_table_results.querys.each do |query| # first round to save adapters without overlap
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@@ -76,6 +90,10 @@ class PluginAbAdapters < Plugin
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76
90
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merge_hits(adapters2,adapters)
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91
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end until (adapters2.count == adapters.count)
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78
92
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|
93
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# puts "MERGED"
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94
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# puts "="*50
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95
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# adapters.each {|a| puts a.inspect}
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96
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+
|
79
97
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max_to_end=@params.get_param('max_ab_to_end').to_i
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80
98
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# type = 'ActionAbAdapter'
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81
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actions=[]
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data/lib/seqtrimnext.rb
CHANGED
metadata
CHANGED
@@ -2,7 +2,7 @@
|
|
2
2
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name: seqtrimnext
|
3
3
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version: !ruby/object:Gem::Version
|
4
4
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prerelease:
|
5
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-
version: 2.0.
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+
version: 2.0.35
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6
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platform: ruby
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7
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authors:
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8
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- Dario Guerrero & Almudena Bocinos
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@@ -10,7 +10,7 @@ autorequire:
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bindir: bin
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11
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cert_chain: []
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12
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|
13
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-
date: 2011-06-
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+
date: 2011-06-22 00:00:00 Z
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14
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dependencies:
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15
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- !ruby/object:Gem::Dependency
|
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16
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name: narray
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