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

Safe HaskellNone




hasNoStops :: GeneticUnit -> CodonTable -> Int -> FastaSequence -> Bool Source #

Remove clone sequences that have stop codons in the first stopRange codons

isInFrame :: FastaSequence -> Bool Source #

Remove out of frame sequences

hasCustomFilter :: Bool -> Maybe Int -> Text -> FastaSequence -> Bool Source #

Remove sequences that do not contain the string customFilter in the customField location, split by "|". Note that this is 1 indexed and 0 means to search the entire header for the customFilter. If the customRemove option is enabled, this function will instead remove sequences that have headers which match the custom filter, as opposed to the other way around (this is defined in the "equal" function). Also takes into account whether to filter on the germline versus the actual sequences.