seqtrimnext 2.0.51 → 2.0.52
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/History.txt +7 -0
- data/Manifest.txt +3 -3
- data/README.rdoc +18 -3
- data/Rakefile +2 -1
- data/bin/parse_params.rb +5 -1
- data/bin/seqtrimnext +53 -21
- data/lib/seqtrimnext/actions/{action_classify.rb → action_user_contaminant.rb} +2 -2
- data/lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb +64 -20
- data/lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb +375 -240
- data/lib/seqtrimnext/classes/extract_stats.rb +26 -23
- data/lib/seqtrimnext/classes/params.rb +109 -123
- data/lib/seqtrimnext/classes/plugin_manager.rb +2 -4
- data/lib/seqtrimnext/classes/seqtrim.rb +24 -29
- data/lib/seqtrimnext/classes/sequence.rb +2 -2
- data/lib/seqtrimnext/classes/sequence_group.rb +21 -1
- data/lib/seqtrimnext/classes/sequence_with_action.rb +25 -13
- data/lib/seqtrimnext/plugins/plugin.rb +42 -12
- data/lib/seqtrimnext/plugins/plugin_ab_adapters.rb +1 -8
- data/lib/seqtrimnext/plugins/plugin_adapters.rb +0 -9
- data/lib/seqtrimnext/plugins/plugin_amplicons.rb +0 -12
- data/lib/seqtrimnext/plugins/plugin_contaminants.rb +5 -8
- data/lib/seqtrimnext/plugins/plugin_extract_inserts.rb +1 -10
- data/lib/seqtrimnext/plugins/plugin_find_poly_at.rb +1 -11
- data/lib/seqtrimnext/plugins/plugin_ignore_repeated.rb +1 -7
- data/lib/seqtrimnext/plugins/plugin_indeterminations.rb +1 -8
- data/lib/seqtrimnext/plugins/plugin_key.rb +1 -9
- data/lib/seqtrimnext/plugins/plugin_linker.rb +0 -9
- data/lib/seqtrimnext/plugins/plugin_low_complexity.rb +6 -21
- data/lib/seqtrimnext/plugins/plugin_low_high_size.rb +3 -13
- data/lib/seqtrimnext/plugins/plugin_low_quality.rb +126 -330
- data/lib/seqtrimnext/plugins/plugin_mids.rb +0 -11
- data/lib/seqtrimnext/plugins/plugin_short_insert.rb +1 -10
- data/lib/seqtrimnext/plugins/plugin_user_contaminants.rb +40 -32
- data/lib/seqtrimnext/plugins/plugin_vectors.rb +0 -9
- data/lib/seqtrimnext/templates/amplicons.txt +1 -8
- data/lib/seqtrimnext/templates/genomics_454.txt +12 -8
- data/lib/seqtrimnext/templates/genomics_454_with_paired.txt +19 -1
- data/lib/seqtrimnext/templates/genomics_short_reads.txt +26 -1
- data/lib/seqtrimnext/templates/genomics_short_reads_2.txt +24 -1
- data/lib/seqtrimnext/templates/only_quality.txt +24 -0
- data/lib/seqtrimnext/templates/sanger.txt +25 -0
- data/lib/seqtrimnext/templates/transcriptomics_454.txt +18 -1
- data/lib/seqtrimnext/templates/transcriptomics_plants.txt +22 -1
- data/lib/seqtrimnext/templates/transcriptomics_short_reads.txt +23 -1
- data/lib/seqtrimnext.rb +1 -1
- metadata +20 -7
- data/lib/seqtrimnext/plugins/plugin_adapters_old.rb +0 -165
- data/lib/seqtrimnext/plugins/plugin_rem_adit_artifacts.rb +0 -245
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require "plugin"
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########################################################
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# Author: Almudena Bocinos Rioboo
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#
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# Defines the main methods that are necessary to execute PluginRemAditArtifacts
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#
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# Inherit: Plugin
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########################################################
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class PluginRemAditArtifacts < Plugin
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# Begins the plugin_low_high_size's execution whit the sequence "seq"
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# Returns a list with start of polyA or polyT seq or 0 if not found
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# start of a possible second polyAT what was found in the second search, since it looks for both
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# Uses the param polyA_length to look for at least that number of contiguous A's
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def execute(seqs)
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seqs.each do |s|
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exec_seq(s)
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end
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end
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def exec_seq(seq)
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$LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: removing artifacts into the sequence"
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seq2 = seq.seq_fasta
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first = 0
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last = seq2.size-1
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old_first=first
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old_last=last
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while (seq2 =~ /^(GCGGGG|CCCCGC)/i)
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first += 6
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seq2.slice!(0..5)
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end
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while (seq2 =~ /(GCGGGG|CCCCGC)$/i)
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last -= 6
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seq2.slice!(seq2.size-1-5..seq2.size-1)
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end
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#is_forward, is_cDNA,
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#TrimExtremeNXs(first,last)
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is_forward = @params.get_param('is_forward')=='true'
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is_cDNA = @params.get_param('is_cDNA')=='true'
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previous_first,previous_last =0,0
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until ((previous_first == first) && (previous_last == last))
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previous_first,previous_last = first, last
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if (is_cDNA)
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if (is_forward)
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nTs = 0
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nTs = $1.length if (seq2 =~ /^(T+)/i)
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if (nTs > 3)
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seq2.slice!(0..nTs -1)
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first += nTs #-1
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end
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nAs = 0
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nAs = $1.length if (seq2 =~ /(A+)$/i)
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if (nAs > 3)
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seq2.slice!(seq2.size - nAs..seq2.size - 1)
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last -= nAs
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end
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else #si es backward
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nTs = 0
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nTs = $1.length if (seq2 =~ /(T+)$/i)
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if (nTs > 3)
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seq2.slice!(seq2.size-nTs..seq2.size-1)
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last -= nTs
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end
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nAs = 0
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nAs = $1.length if (seq2 =~ /^(A+)/i)
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if (nAs > 3)
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seq2.slice!(0..nAs -1)
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first += nAs
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end
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end
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end
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end
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if (((first>=0) && (first>old_first)) || ((last>=0) && (last<old_last)))
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type='ActionRemAditArtifacts'
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actions = []
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# seq.add_action(first,last,type)
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a=seq.new_action(first,last,type)
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actions.push a
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seq.add_actions(actions)
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end
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end
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######################################################################
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#---------------------------------------------------------------------
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def execute_old(seq)
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seq2 = seq.seq_fasta
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#seq2 = 'dGCGGGG'
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first = 0
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last = seq2.size-1
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old_first=first
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old_last=last
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# puts '1 '+seq2
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# puts 'POS '+first.to_s
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# puts 'POS '+last.to_s
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while (seq2 =~ /^(GCGGGG|CCCCGC)/i)
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first += 6
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seq2.slice!(0..5)
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# puts '2 '+seq2
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# already = true
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end
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while (seq2 =~ /(GCGGGG|CCCCGC)$/i)
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last -= 6
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seq2.slice!(seq2.size-1-5..seq2.size-1)
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# puts '3 '+seq2
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# already = true
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end
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#is_forward, is_cDNA,
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#TrimExtremeNXs(first,last)
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is_forward = @params.get_param('is_forward')
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is_cDNA = @params.get_param('is_cDNA')
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# puts '4 '+seq2
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previous_first,previous_last =0,0
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until ((previous_first == first) && (previous_last == last))
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previous_first,previous_last = first, last
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# puts 'POS5-F '+first.to_s
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# puts 'POS5-L '+last.to_s
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if (is_cDNA)
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if (is_forward)
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# puts '5 '+seq2
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nTs = 0
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nTs = $1.length if (seq2 =~ /^(T+)/i)
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if (nTs > 3)
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seq2.slice!(0..nTs -1)
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# puts '6 '+seq2
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first += nTs #-1
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# puts 'POS6-F '+first.to_s
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end
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nAs = 0
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nAs = $1.length if (seq2 =~ /(A+)$/i)
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# puts '6-7 '+seq2 + nAs.to_s
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if (nAs > 3)
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# puts '7 '+seq2
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seq2.slice!(seq2.size - nAs..seq2.size - 1)
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last -= nAs#seq2.size-nAs-2
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# puts 'POS7-L '+last.to_s
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end
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else #si es backward
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# puts '5b '+seq2
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nTs = 0
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nTs = $1.length if (seq2 =~ /(T+)$/i)
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if (nTs > 3)
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# puts '6b '+seq2
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seq2.slice!(seq2.size-nTs..seq2.size-1)
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last -= nTs#seq2.size-nTs -2
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# puts 'POS6b-L '+last.to_s
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end
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nAs = 0
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nAs = $1.length if (seq2 =~ /^(A+)/i)
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if (nAs > 3)
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# puts '7b '+seq2
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seq2.slice!(0..nAs -1)
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first += nAs#nAs -1
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# puts 'POS7b-f '+first.to_s
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end
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end
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end
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end
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#first -= 1 if (old_first!= first)
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#last += 1 if (old_last!= last)
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# puts 'POS7-8 '+first.to_s
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# puts 'POS7-8 '+last.to_s
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if (((first>=0) && (first>old_first)) || ((last>=0) && (last<old_last)))
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type='ActionRemAditArtifacts'
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# puts '8 '+seq2
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seq.add_action(first,last,type)
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end
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# puts '9 '+seq2
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end
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######################################################################
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#---------------------------------------------------------------------
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#Returns an array with the errors due to parameters are missing
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def self.check_params(params)
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errors=[]
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# if !params.exists?('ta')
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# errors.push " The param <ta> doesn't exist"
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# end
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# if !params.exists?('poly_at_length')
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# errors.push " The param <poly_at_length> doesn't exist"
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# end
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return errors
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end
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end
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