pwem.convert.sequence module

class pwem.convert.sequence.SequenceHandler(sequence=None, iUPACAlphabet=0, isAminoacid=True)

Bases: object

alignSeq(referenceSeq)

downloadSeqFromDatabase(seqID)

downloadSeqFromFile(fileName, type='fasta')

saveFile(fileName, seqID, sequence=None, name=None, seqDescription=None, type='fasta')

pwem.convert.sequence.alignBioPairwise2Sequences(structureSequenceId, structureSequence, userSequenceId, userSequence, outFileName)

aligns two sequences and saves them to disk using fasta format

pwem.convert.sequence.alignClustalSequences(inFile, outFile)

pwem.convert.sequence.alignMuscleSequences(inFile, outFile)

pwem.convert.sequence.alphabetToIndex(isAminoacid, alphabet)

pwem.convert.sequence.cleanSequence(alphabet, sequence)

pwem.convert.sequence.cleanSequenceScipion(isAminoacid, iUPACAlphabet, sequence)

pwem.convert.sequence.indexToAlphabet(isAminoacid, iUPACAlphabet)

pwem.convert.sequence.saveFileSequencesToAlign(SeqDic, inFile, type='fasta')

pwem.convert.sequence.sequenceLength(filename, format='fasta')