modify-fasta-0.8.0.3: Modify fasta (and CLIP) files in several optional ways

Safe HaskellNone
LanguageHaskell98

TransformFastaList

Synopsis

Documentation

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