Table of Contents - mgnu-2.1.1 Documentation
Classes and Modules
- MgNu
- MgNu::Alignment
- MgNu::Genbank
- MgNu::Genbank::Feature
- MgNu::Genbank::Location
- MgNu::Genbank::Qualifier
- MgNu::Genbank::Reference
- MgNu::Genbank::Source
- MgNu::Loggable
- MgNu::Logger
- MgNu::Parser
- MgNu::Parser::Blast
- MgNu::Parser::Blast::Format0
- MgNu::Parser::Blast::Format7
- MgNu::Parser::Blast::Format8
- MgNu::Parser::Blast::Hsp
- MgNu::Parser::Blast::Query
- MgNu::Parser::Blast::Sbjct
- MgNu::Parser::ClustalW
- MgNu::Parser::Fasta
- MgNu::Parser::FastaHeaderIndex
- MgNu::Parser::FastaIndex
- MgNu::Parser::Fastq
- MgNu::Parser::GFF
- MgNu::Parser::GFF::Record
- MgNu::Parser::Genbank
- MgNu::Parser::Iprscan
- MgNu::Parser::Iprscan::Hit
- MgNu::Parser::IprscanFile
- MgNu::Parser::KeggOntologyIndex
- MgNu::Parser::Pilercr
- MgNu::Parser::Prodigal
- MgNu::Parser::Prodigal::Sequence
- MgNu::Parser::Sam
- MgNu::Parser::Sam::Alignment
- MgNu::Parser::Sam::Header
- MgNu::Parser::Sam::Pair
- MgNu::Sequence
- MgNu::Sequence::Fasta
- MgNu::Sequence::Fastq
- MgNu::Version
- Nu
- Regexp
- String
Methods
- ::get — MgNu::Logger
- ::log= — MgNu::Logger
- ::new — MgNu::Alignment
- ::new — MgNu::Genbank
- ::new — MgNu::Genbank::Feature
- ::new — MgNu::Genbank::Location
- ::new — MgNu::Genbank::Qualifier
- ::new — MgNu::Genbank::Reference
- ::new — MgNu::Genbank::Source
- ::new — MgNu::Parser::Blast
- ::new — MgNu::Parser::Blast::Format0
- ::new — MgNu::Parser::Blast::Format7
- ::new — MgNu::Parser::Blast::Format8
- ::new — MgNu::Parser::Blast::Hsp
- ::new — MgNu::Parser::Blast::Query
- ::new — MgNu::Parser::Blast::Sbjct
- ::new — MgNu::Parser::ClustalW
- ::new — MgNu::Parser::Fasta
- ::new — MgNu::Parser::FastaHeaderIndex
- ::new — MgNu::Parser::FastaIndex
- ::new — MgNu::Parser::Fastq
- ::new — MgNu::Parser::Genbank
- ::new — MgNu::Parser::GFF
- ::new — MgNu::Parser::GFF::Record
- ::new — MgNu::Parser::Iprscan::Hit
- ::new — MgNu::Parser::IprscanFile
- ::new — MgNu::Parser::KeggOntologyIndex
- ::new — MgNu::Parser::Pilercr
- ::new — MgNu::Parser::Prodigal
- ::new — MgNu::Parser::Prodigal::Sequence
- ::new — MgNu::Parser::Sam
- ::new — MgNu::Parser::Sam::Alignment
- ::new — MgNu::Parser::Sam::Header
- ::new — MgNu::Parser::Sam::Pair
- ::new — MgNu::Sequence
- ::new — MgNu::Sequence::Fasta
- ::new — MgNu::Sequence::Fastq
- ::parse — MgNu::Genbank::Feature
- ::parse — MgNu::Genbank::Reference
- ::parse — MgNu::Genbank::Source
- ::to_s — MgNu::Version
- #[] — MgNu::Alignment
- #[] — MgNu::Parser::FastaHeaderIndex
- #[] — MgNu::Parser::FastaIndex
- #[] — MgNu::Parser::KeggOntologyIndex
- #aa? — MgNu::Sequence
- #aminoacid? — MgNu::Sequence
- #attributes= — MgNu::Parser::Sam::Alignment
- #best_hit — MgNu::Parser::Blast::Query
- #best_hsp — MgNu::Parser::Blast::Sbjct
- #bit_score — MgNu::Parser::Blast::Sbjct
- #buidup_sequence_from_parts — MgNu::Genbank::Location
- #build_sequence — MgNu::Genbank::Location
- #close — MgNu::Parser::FastaHeaderIndex
- #close — MgNu::Parser::FastaIndex
- #close — MgNu::Parser::KeggOntologyIndex
- #complement — MgNu::Sequence
- #complement! — MgNu::Sequence
- #debug — MgNu::Loggable
- #distance — MgNu::Sequence
- #dna? — MgNu::Sequence
- #each — MgNu::Alignment
- #each — MgNu::Parser::Blast
- #each — MgNu::Parser::Blast::Format8
- #each — MgNu::Parser::Fasta
- #each — MgNu::Parser::Fastq
- #each — MgNu::Parser::GFF
- #each — MgNu::Parser::KeggOntologyIndex
- #each — MgNu::Parser::Pilercr
- #each — MgNu::Parser::Prodigal
- #each — MgNu::Parser::Sam
- #each_position — MgNu::Alignment
- #end_element — MgNu::Parser::Blast::Format7
- #error — MgNu::Loggable
- #evalue — MgNu::Parser::Blast::Sbjct
- #extract_all_hsps — MgNu::Parser::Blast::Format0
- #extract_dbinfo — MgNu::Parser::Blast::Format0
- #extract_hsp — MgNu::Parser::Blast::Format8
- #extract_query — MgNu::Parser::Blast::Format0
- #extract_sbjct — MgNu::Parser::Blast::Format0
- #extract_sbjct — MgNu::Parser::Blast::Format8
- #fatal — MgNu::Loggable
- #gc_content — MgNu::Sequence
- #get_sequence — MgNu::Genbank::Location
- #global_match — Regexp
- #identity — MgNu::Parser::Blast::Sbjct
- #identity — MgNu::Sequence
- #info — MgNu::Loggable
- #length — MgNu::Sequence
- #level — MgNu::Logger
- #levenshtein_distance — MgNu::Sequence
- #match — MgNu::Alignment
- #match_length — MgNu::Parser::Iprscan::Hit
- #method_missing — MgNu::Genbank::Feature
- #nblocks — MgNu::Sequence
- #parse — MgNu::Parser::Blast
- #parse — MgNu::Parser::Blast::Format0
- #parse — MgNu::Parser::Blast::Format8
- #parse — MgNu::Parser::ClustalW
- #parse — MgNu::Parser::FastaHeaderIndex
- #parse — MgNu::Parser::FastaIndex
- #parse — MgNu::Parser::Genbank
- #parse — MgNu::Parser::IprscanFile
- #parse — MgNu::Parser::KeggOntologyIndex
- #parse — MgNu::Parser::Prodigal
- #parse_attributes — MgNu::Parser::GFF::Record
- #parse_features — MgNu::Parser::Genbank
- #parse_features — MgNu::Parser::Prodigal::Sequence
- #parse_ko_buffer — MgNu::Parser::KeggOntologyIndex
- #parse_raw_value — MgNu::Genbank::Location
- #parse_references — MgNu::Parser::Genbank
- #parse_section — MgNu::Parser::Genbank
- #parse_sequence — MgNu::Parser::Genbank
- #parse_until — MgNu::Parser
- #percent_identity — MgNu::Sequence
- #print_multiline — String
- #process_buffer — MgNu::Parser::Blast::Format0
- #process_buffer — MgNu::Parser::Pilercr
- #process_header — MgNu::Parser::Sam
- #process_hsp — MgNu::Parser::Blast::Format0
- #protein? — MgNu::Sequence
- #query_frameshifts — MgNu::Parser::Blast::Hsp
- #revcomp — MgNu::Sequence
- #revcomp! — MgNu::Sequence
- #reverse_complement — MgNu::Sequence
- #reverse_complement! — MgNu::Sequence
- #rna? — MgNu::Sequence
- #sequence_by_columns — MgNu::Sequence::Fasta
- #set_basic_properties — MgNu::Genbank::Location
- #set_properties_for_join_types — MgNu::Genbank::Location
- #split_at_features — MgNu::Parser::Genbank
- #split_at_features — MgNu::Parser::Prodigal::Sequence
- #split_at_header_tag — MgNu::Parser::Genbank
- #split_on_n — MgNu::Sequence::Fasta
- #start_element — MgNu::Parser::Blast::Format7
- #strip_quotes — MgNu::Parser
- #summary — MgNu::Parser::Iprscan::Hit
- #text — MgNu::Parser::Blast::Format7
- #to_fasta — MgNu::Sequence::Fastq
- #to_genbank — MgNu::Sequence
- #to_s — MgNu::Alignment
- #to_s — MgNu::Genbank
- #to_s — MgNu::Genbank::Feature
- #to_s — MgNu::Genbank::Location
- #to_s — MgNu::Genbank::Qualifier
- #to_s — MgNu::Genbank::Reference
- #to_s — MgNu::Genbank::Source
- #to_s — MgNu::Parser::Iprscan::Hit
- #to_s — MgNu::Parser::Prodigal::Sequence
- #to_s — MgNu::Sequence
- #to_s — MgNu::Sequence::Fasta
- #to_s — MgNu::Sequence::Fastq
- #translate — MgNu::Sequence
- #translate! — MgNu::Sequence
- #unknown — MgNu::Loggable
- #unpack_quality — MgNu::Sequence::Fastq
- #warn — MgNu::Loggable