| Safe Haskell | None |
|---|---|
| Language | Haskell98 |
TransformFastaList
- convertToAminoAcidsFastaSequence :: FastaSequence -> FastaSequence
- replaceChars :: Char -> Text -> Text -> Text
- fillInSequence :: Field -> Start -> Char -> FastaSequence -> FastaSequence
- changeField :: Maybe Field -> Text -> FastaSequence -> FastaSequence
- changeAllFields :: FastaSequence -> [(Maybe Int, Text)] -> FastaSequence
- getRegionSequence :: Maybe Start -> Maybe Stop -> FastaSequence -> FastaSequence
- trimFasta :: GeneticUnit -> Maybe Frame -> Maybe Frame -> FastaSequence -> FastaSequence
- removeUnknownNucs :: FastaSequence -> FastaSequence
Documentation
convertToAminoAcidsFastaSequence :: FastaSequence -> FastaSequence Source
Convert sequences to amino acids
fillInSequence :: Field -> Start -> Char -> FastaSequence -> FastaSequence Source
Fill in the sequence with corrected nucleotides or amino acids
changeField :: Maybe Field -> Text -> FastaSequence -> FastaSequence Source
Change a field to a match, so a regex "ch.*_" to field 2 of ">abc|brie_cheese_dude" would result in ">abc|cheese_". Useful for getting specific properties from a field
changeAllFields :: FastaSequence -> [(Maybe Int, Text)] -> FastaSequence Source
Change all fields to their matches based on changeField
getRegionSequence :: Maybe Start -> Maybe Stop -> FastaSequence -> FastaSequence Source
Get a region of a sequence, 1 indexed
trimFasta :: GeneticUnit -> Maybe Frame -> Maybe Frame -> FastaSequence -> FastaSequence Source
Trim off extra nucleotides (or amino acids) from a fasta sequence. If inframe and outframe are specified, instead cut off based on those frames.
removeUnknownNucs :: FastaSequence -> FastaSequence Source
Convert non standard nucleotides to gaps