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

Safe HaskellNone




isRight' :: Either a b -> Bool Source #

Check if the data structure is Right

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