Safe Haskell | None |
---|---|
Language | Haskell98 |
- isRight' :: Either a b -> Bool
- listToMaybe' :: [a] -> Maybe [a]
- filterHighlyMutated :: GeneticUnit -> CodonTable -> CloneMap -> (CloneMap, Maybe String)
- removeCodonMutCount :: CodonMut -> Text -> Text -> CloneMap -> CloneMap
- removeStopsCloneMap :: GeneticUnit -> CodonTable -> Int -> CloneMap -> (CloneMap, Maybe String)
- removeDuplicatesCloneMap :: CloneMap -> CloneMap
- removeOutOfFrameSeqs :: CloneMap -> CloneMap
- removeCustomFilter :: Bool -> Bool -> Maybe Int -> Text -> CloneMap -> CloneMap
- removeAllCustomFilters :: Bool -> Bool -> CloneMap -> [(Maybe Int, Text)] -> CloneMap
- removeEmptyClone :: CloneMap -> CloneMap
- convertToAminoAcidsCloneMap :: CodonTable -> CloneMap -> (CloneMap, Maybe String)
Documentation
listToMaybe' :: [a] -> Maybe [a] Source
Altered version of listToMaybe
filterHighlyMutated :: GeneticUnit -> CodonTable -> CloneMap -> (CloneMap, Maybe String) Source
Remove highly mutated sequences (sequences with more than a third of their sequence being mutated).
removeCodonMutCount :: CodonMut -> Text -> Text -> CloneMap -> CloneMap Source
Replace codons that have more than CodonMut mutations (make them "---" codons).
removeStopsCloneMap :: GeneticUnit -> CodonTable -> Int -> CloneMap -> (CloneMap, Maybe String) Source
Remove clone sequences that have stop codons in the first stopRange codons
removeDuplicatesCloneMap :: CloneMap -> CloneMap Source
Remove duplicate sequences
removeOutOfFrameSeqs :: CloneMap -> CloneMap Source
Remove out of frame sequences
removeCustomFilter :: Bool -> Bool -> Maybe Int -> Text -> CloneMap -> CloneMap 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.
removeEmptyClone :: CloneMap -> CloneMap Source
Remove clones that do not have any sequences after the filtrations
convertToAminoAcidsCloneMap :: CodonTable -> CloneMap -> (CloneMap, Maybe String) Source
Convert sequences to amino acids