!"#$%&'()*+,-./0123456 7 8 9 : ; < = > ? @ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z [\]^_`abcdefghijklmnopqrstuvwxyz{|}~SafeIDefines the rules for complement. Unknown characters are left untouched.SafeXA clone is a collection of sequences derived from a germline with a specific identifier      NoneVGets a 1 indexed field from the header of a fasta sequence using a certain delimiter.$Gets the complement of the sequence.,Gets the reverse complement of the sequence.Safe<Converts a codon to an amino acid Remember, if there is an NM in that DNA sequence, then it is translated as an X, an unknown amino acid.&Translate a codon using a custom tableTranslates a text of nucleotides given a reading frame (1, 2, or 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns a text with the error if the codon is invalid. Also has customized codon translations as well overriding the defaults.Translates a text of nucleotides given a reading frame (1, 2, or 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns a text with the error if the codon is invalid.NoneParse a standard fasta fileParse a CLIP fasta fileattopares any char but space"attoparsec parser for a fasta type"attoparsec parser for a fasta file+attoparsec parser for a CLIP fasta sequence"attoparsec parser for a fasta fileParse a standard fasta fileParse a CLIP fasta file'Parse a standard fasta file into a pipe#Parse a CLIP fasta file into a pipe(Remove Ns from a collection of sequencesRemove Ns from a sequence3Remove Ns from a collection of CLIP fasta sequences  Safe"XA clone is a collection of sequences derived from a germline with a specific identifier !"#$%&'()*+ !"#$%&'()* '()*&%$#" !+ !"#$%&'()*+None/VGets a 1 indexed field from the header of a fasta sequence using a certain delimiter.0$Gets the complement of the sequence.1,Gets the reverse complement of the sequence./01/01/01/01Safe2<Converts a codon to an amino acid Remember, if there is an NM in that DNA sequence, then it is translated as an X, an unknown amino acid.3&Translate a codon using a custom table4Translates a text of nucleotides given a reading frame (1, 2, or 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns a text with the error if the codon is invalid. Also has customized codon translations as well overriding the defaults.5Translates a text of nucleotides given a reading frame (1, 2, or 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns a text with the error if the codon is invalid.2345234523542345 None6Parse a standard fasta file7Parse a CLIP fasta fileattopares any char but space"attoparsec parser for a fasta type"attoparsec parser for a fasta file+attoparsec parser for a CLIP fasta sequence"attoparsec parser for a fasta file8Parse a standard fasta file9Parse a CLIP fasta file:'Parse a standard fasta file into a pipe;#Parse a CLIP fasta file into a pipe<(Remove Ns from a collection of sequences=Remove Ns from a sequence>3Remove Ns from a collection of CLIP fasta sequences6789:;<=> 6789:;<=> 6789:;<=>6789:;<=>None !"#$%&'()*/0123456789:;<=>None  SafeAXA clone is a collection of sequences derived from a germline with a specific identifier ?@ABCDEFGHIJ ?@ABCDEFGHI FGHIEDCBA?@J?@ABCDEFGHIJ NoneNVGets a 1 indexed field from the header of a fasta sequence using a certain delimiter.O$Gets the complement of the sequence.P,Gets the reverse complement of the sequence.NOPNOPNOPNOP SafeQ<Converts a codon to an amino acid Remember, if there is an NM in that DNA sequence, then it is translated as an X, an unknown amino acid.R&Translate a codon using a custom tableSTranslates a string of nucleotides given a reading frame (1, 2, or 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns a string with the error if the codon is invalid. Also has customized codon translations as well overriding the defaults.TTranslates a string of nucleotides given a reading frame (1, 2, or 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns a string with the error if the codon is invalid.QRSTQRSTQRTSQRST SafeU1Parse a standard fasta file into string sequencesV-Parse a CLIP fasta file into string sequencesWParse a standard fasta file into string sequences for pipes. This is the highly recommeded way of parsing, as it is computationally fast and uses constant file memoryX(Remove Ns from a collection of sequencesYRemove Ns from a sequenceZ3Remove Ns from a collection of CLIP fasta sequences UVWXYZUVWXYZUVWXYZ UVWXYZNone?@ABCDEFGHINOPQRSTUVWXYZSafe_+Returns the hydrophobicity of an amino acid[\]^_[\]^_[\]^_[\]^_SafefXA clone is a collection of sequences derived from a germline with a specific identifier defghijklmno defghijklmn klmnjihgfdeodefghijklmnoNonesVGets a 1 indexed field from the header of a fasta sequence using a certain delimiter.t$Gets the complement of the sequence.u,Gets the reverse complement of the sequence.stustustustuSafevByteString version of chunksOfw<Converts a codon to an amino acid Remember, if there is an NM in that DNA sequence, then it is translated as an X, an unknown amino acid.x&Translate a codon using a custom tabley Translates a bytestring of nucleotides given a reading frame (1, 2, or 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns a bytestring with the error if the codon is invalid. Also has customized codon translations as well overriding the defaults.zTranslates a bytestring of nucleotides given a reading frame (1, 2, or 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns a bytestring with the error if the codon is invalid.vwxyzvwxyzvwxzyvwxyzNone{/Parse a standard fasta file into text sequences|+Parse a CLIP fasta file into text sequencesattopares any char but space"attoparsec parser for a fasta type"attoparsec parser for a fasta file+attoparsec parser for a CLIP fasta sequence"attoparsec parser for a fasta file}Parse a standard fasta file~+Parse a CLIP fasta file into text sequencesParse a standard fasta file into strict text sequences for pipes. This is the highly recommeded way of parsing, as it is computationally fast and uses memory based on line length=Parse a CLIP fasta file into strict text sequences for pipes.(Remove Ns from a collection of sequencesRemove Ns from a sequence3Remove Ns from a collection of CLIP fasta sequences{|}~ {|}~ {|}~{|}~SafeXA clone is a collection of sequences derived from a germline with a specific identifier NoneVGets a 1 indexed field from the header of a fasta sequence using a certain delimiter.$Gets the complement of the sequence.,Gets the reverse complement of the sequence.Safe#Lazy ByteString version of chunksOf<Converts a codon to an amino acid Remember, if there is an NM in that DNA sequence, then it is translated as an X, an unknown amino acid.&Translate a codon using a custom table Translates a bytestring of nucleotides given a reading frame (1, 2, or 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns a bytestring with the error if the codon is invalid. Also has customized codon translations as well overriding the defaults.Translates a bytestring of nucleotides given a reading frame (1, 2, or 3) -- drops the first 0, 1, or 2 nucleotides respectively. Returns a bytestring with the error if the codon is invalid.None Parse a standard fasta file intoParse a CLIP fasta file intoattopares any char but space"attoparsec parser for a fasta type"attoparsec parser for a fasta file+attoparsec parser for a CLIP fasta sequence"attoparsec parser for a fasta fileParse a standard fasta file+Parse a CLIP fasta file into text sequences'Parse a standard fasta file into a pipe=Parse a CLIP fasta file into strict text sequences for pipes.(Remove Ns from a collection of sequencesRemove Ns from a sequence3Remove Ns from a collection of CLIP fasta sequences NoneNonedefghijklmnstuvwxyz{|}~ !"#$$%&'()*+,-./0123456789: !"#$$%&'()*+,-./01 2 3 4 5 6 7 8 9 :     ! " # $ $ % & ' ( ) * + , - . / 0 1 ; < 6 8 9 :=>?@ABCDE !"#$$%&'()*+,-F./0123456789: !"#$$%&'()*+,-F./0123456789:GHIJKLMNOPQR G H I J K L M N O P Q R L M N O P QGHIJKLMNOPQRGHIJKLMNOPQRS%fasta-0.10.4.2-5uZM2nUd8HuH6icBCZBOyEData.Fasta.UtilityData.Fasta.Text.TypesData.Fasta.Text.UtilityData.Fasta.Text.TranslationData.Fasta.Text.ParseData.Fasta.Text.Lazy.TypesData.Fasta.Text.Lazy.Utility Data.Fasta.Text.Lazy.TranslationData.Fasta.Text.Lazy.ParseData.Fasta.String.TypesData.Fasta.String.UtilityData.Fasta.String.TranslationData.Fasta.String.ParseData.Fasta.CategoryData.Fasta.ByteString.TypesData.Fasta.ByteString.Utility!Data.Fasta.ByteString.TranslationData.Fasta.ByteString.Parse Data.Fasta.ByteString.Lazy.Types"Data.Fasta.ByteString.Lazy.Utility&Data.Fasta.ByteString.Lazy.Translation Data.Fasta.ByteString.Lazy.ParseData.Fasta.Text.LazyData.Fasta.TextData.Fasta.StringData.Fasta.ByteString.LazyData.Fasta.ByteString complRules ShowFasta showFastaCloneMapGermlineCloneAACodon FastaSequence fastaHeaderfastaSeq$fShowFastaFastaSequence$fEqFastaSequence$fOrdFastaSequence$fShowFastaSequencegetFieldcomplrevComplcodon2aacustomCodon2aacustomTranslate translate parsecFastaparsecCLIPFasta attoFasta attoCLIPFasta pipesFastapipesCLIPFastaremoveNsremoveN removeCLIPNs parseFastaparseCLIPFastaHydrophobicity HydrophobicNeutral HydrophilicaaToHydrophobicity$fEqHydrophobicity$fOrdHydrophobicity$fReadHydrophobicity$fShowHydrophobicitychunksOf anyButSpacefasta' fastaFile' fastaCLIP'fastaCLIPFile'eoleoefasta fastaFile fastaCLIP fastaCLIPFileclone'