cutNs

Function

cutNs

Cut out all masked sequences from a Dna5String.

cutNs(sequenceCut, sequence)

Include Headers

seqan/alignment_free.h

Parameters

sequenceCut	Dna5String similar to sequence with all Ns cut out Types: Dna5String
sequence	Masked DNA sequence. Types: Dna5String

Remarks

This function concatenates the nonmasked parts of the sequence, thereby changing the word content. If you want to remove the masked parts of a sequence without concatenation, use stringToStringSet.

Return Values

Returns a Dna5String similar to the input sequence with all Ns cut out.

Examples

Transform a masked DNA sequence into an unmasked sequences with all masked parts cut out

using namespace seqan;
Dna5String sequenceMasked =
"NNNNNNTTTCCGAAAAGGTANNNNNGCAACTTTANNNCGTGATCAAAGTTTTCCCCGTCGAAATTGGGNNTG";
Dna5String sequenceMaskedPartsRemoved;
cutNs(sequenceMaskedPartsRemoved, sequenceMasked);
// Print the masked sequence
std::cout<<sequenceMasked<<"\n";
// Print the sequence with the masked parts removed
std::cout<<sequenceMaskedPartsRemoved<<"\n";
// sequenceMasked =
// "NNNNNNTTTCCGAAAAGGTANNNNNGCAACTTTANNNCGTGATCAAAGTTTTCCCCGTCGAAATTGGGNNTG"
// sequenceMaskedPartsRemoved =
// "TTTCCGAAAAGGTAGCAACTTTACGTGATCAAAGTTTTCCCCGTCGAAATTGGGTG"