Method List

Classes Methods Files

Search:

#& BioDSL::CAry
#+ BioDSL::Pipeline
#+ BioDSL::Seq
#<< BioDSL::Pipeline
#<< BioDSL::Seq
#<< BioDSL::Serializer
#[] BioDSL::SliceAlign::PosIndex
#[] BioDSL::Taxonomy::Index::TaxNode
#[] BioDSL::Seq
#[]= BioDSL::Taxonomy::Index::TaxNode
#[]= BioDSL::Seq
#^ BioDSL::CAry
#add BioDSL::Taxonomy::Index
#add_ambiguity_macro BioDSL::Ambiguity
#ary BioDSL::CAry
#aux_exist BioDSL::AuxHelper
#calc_delta BioDSL::Command
#calc_diff BioDSL::Assemble
#calc_overlap BioDSL::Assemble
#calc_time_elapsed BioDSL::Command
#call BioDSL::Command
check_name_pair BioDSL::Seq
#check_options BioDSL::Assemble
check_strings BioDSL::Hamming
#children BioDSL::Taxonomy::Index::TaxNode
#children_ids BioDSL::Taxonomy::Index::TaxNode
#close BioDSL::Filesys
#close BioDSL::Stream
#closed? BioDSL::Stream
#cluster_otus BioDSL::Usearch
cluster_otus BioDSL::Usearch
cluster_smallmem BioDSL::Usearch
#cluster_smallmem BioDSL::Usearch
#commands BioDSL::Pipeline
#commify Numeric
#complement BioDSL::Seq
#complement! BioDSL::Seq
#complete BioDSL::Pipeline
#compose_mail BioDSL::EmailHelper
#composition BioDSL::Seq
#convert_types Array
#count BioDSL::CAry
create BioDSL::TmpDir
debug BioDSL
debug= BioDSL
dist_point2line BioDSL::Math
dist_point2point BioDSL::Math
distance BioDSL::Levenshtein
distance BioDSL::Hamming
#dna? BioDSL::Seq
#each BioDSL::Channel
#each BioDSL::Fastq::IO
#each BioDSL::Filesys
#each BioDSL::Fasta::IO
#each BioDSL::Fastq
#each BioDSL::Fasta
#each BioDSL::Stream
#each BioDSL::Serializer
#each BioDSL::Usearch::IO
#each_array BioDSL::CSV
#each_digest BioDSL::Digest
#each_hash BioDSL::CSV
#each_homopolymer BioDSL::Homopolymer
each_mem BioDSL::Mummer
#each_mem BioDSL::Mummer
#each_orf BioDSL::Seq
#each_uc BioDSL::Usearch::IO
#edit_distance BioDSL::Seq
#entry BioDSL::Seq::Orf
#entry_left BioDSL::Assemble
#entry_overlap BioDSL::Assemble
#entry_right BioDSL::Assemble
#eof? BioDSL::Filesys
execute BioDSL::Fork
#execute BioDSL::Taxonomy::Search
#execute BioDSL::Fork
#fill BioDSL::CAry
#fill! BioDSL::CAry
#generate BioDSL::Seq
generate_oligos BioDSL::Seq
#get_node BioDSL::Taxonomy::Index
#gets BioDSL::CSV::IO
#gets BioDSL::Filesys
#hamming_distance BioDSL::Seq
#hard_mask BioDSL::Seq
#indels BioDSL::Seq
#indels_remove BioDSL::Seq
#initialize BioDSL::PlotMatches
#initialize BioDSL::AssembleSeqIdba
#initialize BioDSL::ReadTable
#initialize BioDSL::Taxonomy::Search
#initialize BioDSL::Fork
#initialize BioDSL::TrimPrimer
#initialize BioDSL::CollectOtus
#initialize BioDSL::PlotResidueDistribution
#initialize BioDSL::Taxonomy::Search::TaxPath
#initialize BioDSL::CAry
#initialize BioDSL::DereplicateSeq
#initialize BioDSL::UniqueValues
#initialize BioDSL::Dump
#initialize BioDSL::Fasta
#initialize BioDSL::Taxonomy::Index::TaxNode
#initialize BioDSL::Count
#initialize BioDSL::Random
#initialize BioDSL::Fastq
#initialize BioDSL::Genecall
#initialize BioDSL::UsearchGlobal
#initialize BioDSL::CollapseOtus
#initialize BioDSL::HtmlReport
#initialize BioDSL::Serializer
#initialize BioDSL::CountValues
#initialize BioDSL::FilterRrna
#initialize BioDSL::WriteTree
#initialize BioDSL::BackTrack::Match
#initialize BioDSL::MeanScores
#initialize BioDSL::WriteFasta
#initialize BioDSL::SplitValues
#initialize BioDSL::ReadFasta
#initialize BioDSL::ClusterOtus
#initialize BioDSL::AssembleSeqRay
#initialize BioDSL::AddKey
#initialize BioDSL::ComplementSeq
#initialize BioDSL::AssemblePairs
#initialize BioDSL::SliceAlign
#initialize BioDSL::ReadFastq
#initialize BioDSL::Uclust
#initialize BioDSL::Assemble
#initialize BioDSL::Seq
#initialize BioDSL::UsearchLocal
#initialize BioDSL::UchimeRef
#initialize BioDSL::MergeTable
#initialize BioDSL::Sort
#initialize BioDSL::CSV
#initialize BioDSL::AssembleSeqSpades
#initialize BioDSL::ClassifySeq
#initialize BioDSL::PlotScores
#initialize BioDSL::SliceSeq
#initialize BioDSL::Grab
#initialize BioDSL::MergePairSeq
#initialize BioDSL::Pipeline
#initialize BioDSL::Command
#initialize BioDSL::PlotHistogram
#initialize BioDSL::AlignSeqMothur
#initialize BioDSL::MaskSeq
#initialize BioDSL::Filesys
#initialize BioDSL::AnalyzeResidueDistribution
#initialize BioDSL::ClipPrimer
#initialize BioDSL::WriteTable
#initialize BioDSL::PlotHeatmap
#initialize BioDSL::Channel
#initialize BioDSL::WriteFastq
#initialize BioDSL::SplitPairSeq
#initialize BioDSL::Stream
#initialize BioDSL::Mummer
#initialize BioDSL::SliceAlign::PosIndex
#initialize BioDSL::IndexTaxonomy
#initialize BioDSL::Taxonomy::Index
#initialize BioDSL::DegapSeq
#initialize BioDSL::Usearch
#initialize BioDSL::TrimSeq
#initialize BioDSL::MergeValues
#initialize BioDSL::ReverseSeq
#initialize BioDSL::ClassifySeqMothur
#input BioDSL::Fork
#io BioDSL::Filesys
#kmers BioDSL::Taxonomy::Index::TaxNode
#length BioDSL::BackTrack::Match
#length BioDSL::Homopolymer::Homopolymer
#length BioDSL::Seq
#level BioDSL::Taxonomy::Index::TaxNode
#lmb BioDSL::AssembleSeqRay
#lmb BioDSL::AlignSeqMothur
#lmb BioDSL::ClassifySeq
#lmb BioDSL::CountValues
#lmb BioDSL::DereplicateSeq
#lmb BioDSL::ClassifySeqMothur
#lmb BioDSL::UsearchLocal
#lmb BioDSL::MergePairSeq
#lmb BioDSL::PlotResidueDistribution
#lmb BioDSL::ClipPrimer
#lmb BioDSL::AddKey
#lmb BioDSL::AssembleSeqSpades
#lmb BioDSL::PlotHeatmap
#lmb BioDSL::Genecall
#lmb BioDSL::PlotMatches
#lmb BioDSL::WriteTree
#lmb BioDSL::SliceAlign
#lmb BioDSL::TrimSeq
#lmb BioDSL::Count
#lmb BioDSL::Dump
#lmb BioDSL::FilterRrna
#lmb BioDSL::SliceSeq
#lmb BioDSL::MergeValues
#lmb BioDSL::WriteFastq
#lmb BioDSL::Grab
#lmb BioDSL::MeanScores
#lmb BioDSL::IndexTaxonomy
#lmb BioDSL::AssembleSeqIdba
#lmb BioDSL::SplitValues
#lmb BioDSL::AnalyzeResidueDistribution
#lmb BioDSL::CollapseOtus
#lmb BioDSL::MaskSeq
#lmb BioDSL::ClusterOtus
#lmb BioDSL::PlotScores
#lmb BioDSL::WriteFasta
#lmb BioDSL::TrimPrimer
#lmb BioDSL::UchimeRef
#lmb BioDSL::ReadFasta
#lmb BioDSL::Sort
#lmb BioDSL::SplitPairSeq
#lmb BioDSL::AssemblePairs
#lmb BioDSL::ComplementSeq
#lmb BioDSL::DegapSeq
#lmb BioDSL::UsearchGlobal
#lmb BioDSL::CollectOtus
#lmb BioDSL::WriteTable
#lmb BioDSL::UniqueValues
#lmb BioDSL::PlotHistogram
#lmb BioDSL::ReadFastq
#lmb BioDSL::ReverseSeq
#lmb BioDSL::ReadTable
#lmb BioDSL::MergeTable
#lmb BioDSL::Random
#lmb BioDSL::Uclust
#log_error BioDSL::LogHelper
#log_ok BioDSL::LogHelper
#mask_seq_hard! BioDSL::Seq
#mask_seq_soft! BioDSL::Seq
#match BioDSL::Assemble
#match BioDSL::BackTrack::Match
#merge_overlap BioDSL::Assemble
#name BioDSL::Command
#name BioDSL::Taxonomy::Index::TaxNode
new_bp BioDSL::Seq
#next_entry BioDSL::Fasta
#next_entry BioDSL::Fastq
#next_entry BioDSL::Serializer
#node_id BioDSL::Taxonomy::Index::TaxNode
#node_id BioDSL::Taxonomy::Index
#nodes BioDSL::Taxonomy::Search::TaxPath
open BioDSL::Usearch
open BioDSL::Filesys
open BioDSL::Fastq
open BioDSL::Fasta
open BioDSL::CSV
#options BioDSL::Command
#output BioDSL::Fork
pair BioDSL::Channel
pair BioDSL::Assemble
#parent BioDSL::Taxonomy::Index::TaxNode
#parent_id BioDSL::Taxonomy::Index::TaxNode
#patmatch BioDSL::BackTrack
#patmatch BioDSL::Dynamic
#patscan BioDSL::BackTrack
#patscan BioDSL::Dynamic
#pattern BioDSL::Homopolymer::Homopolymer
pipe BioDSL::Stream
#pop BioDSL::Pipeline
#pos BioDSL::Homopolymer::Homopolymer
#pos BioDSL::BackTrack::Match
#protein? BioDSL::Seq
#puts BioDSL::Filesys
#puts BioDSL::Fasta
#q_end BioDSL::Mummer::Match
#qual BioDSL::Seq
#qual_base33? BioDSL::Seq
#qual_base64? BioDSL::Seq
#qual_coerce! BioDSL::Seq
#qual_convert! BioDSL::Seq
#qual_valid? BioDSL::Seq
#quality_trim BioDSL::Trim
#quality_trim! BioDSL::Trim
#quality_trim_left BioDSL::Trim
#quality_trim_left! BioDSL::Trim
#quality_trim_right BioDSL::Trim
#quality_trim_right! BioDSL::Trim
#read BioDSL::Filesys
#read BioDSL::Stream
#read BioDSL::Channel
read BioDSL::Fasta
#read BioDSL::Fork
read_array BioDSL::CSV
read_hash BioDSL::CSV
retrieve BioDSL::CAry
#reverse BioDSL::Seq
#reverse! BioDSL::Seq
#rna? BioDSL::Seq
#run BioDSL::Pipeline
#run_status BioDSL::Command
#running? BioDSL::Fork
#s_end BioDSL::Mummer::Match
#save BioDSL::Taxonomy::Index
#save_history BioDSL::HistoryHelper
#scores_max BioDSL::Seq
#scores_mean BioDSL::Seq
#scores_mean_local BioDSL::Seq
#scores_min BioDSL::Seq
#send_email BioDSL::EmailHelper
#seq BioDSL::Fasta
#seq BioDSL::Seq
#seq_id BioDSL::Taxonomy::Index::TaxNode
#seq_name BioDSL::Fasta
#seq_name BioDSL::Seq
#shuffle BioDSL::Seq
#shuffle! BioDSL::Seq
#size BioDSL::Pipeline
#size BioDSL::CAry
#skip BioDSL::CSV
#soft_mask BioDSL::Seq
#start BioDSL::BackTrack::Match
#start BioDSL::Seq::Orf
#status BioDSL::Pipeline
#status BioDSL::Command
#status_init BioDSL::StatusHelper
#status_progress BioDSL::StatusHelper
#stop BioDSL::BackTrack::Match
#stop BioDSL::Seq::Orf
store BioDSL::CAry
#taxonomy_backtrack BioDSL::Taxonomy::Search::TaxPath
#terminate BioDSL::Channel
test BioDSL
test= BioDSL
tmpfile BioDSL::Filesys
#to_bp BioDSL::Seq
#to_dna BioDSL::Seq
#to_fasta BioDSL::Seq
#to_fastq BioDSL::Seq
#to_html BioDSL::HtmlReport
#to_key BioDSL::Seq
#to_kmers BioDSL::Kmer
#to_num String
to_oligos BioDSL::Kmer
#to_rna BioDSL::Seq
#to_s BioDSL::BackTrack::Match
#to_s BioDSL::Taxonomy::Search::TaxPath
#to_s BioDSL::Command
#to_s BioDSL::Pipeline
#to_s BioDSL::CAry
#translate BioDSL::Translate
#translate! BioDSL::Translate
#tree_union BioDSL::Taxonomy::Index
#type BioDSL::Seq
#type_guess BioDSL::Seq
#type_guess! BioDSL::Seq
#uchime_ref BioDSL::Usearch
uchime_ref BioDSL::Usearch
#usearch_global BioDSL::Usearch
usearch_global BioDSL::Usearch
#usearch_local BioDSL::Usearch
usearch_local BioDSL::Usearch
verbose BioDSL
verbose= BioDSL
#wait BioDSL::Fork
which BioDSL::Filesys
#write BioDSL::Filesys
#write BioDSL::Channel
#write BioDSL::Stream
#write BioDSL::Fork
#zero BioDSL::CAry
#zero! BioDSL::CAry
#| BioDSL::CAry
#~ BioDSL::CAry