writeAll

Function

writeAll

Write sequence records from to a SequenceStream object.

The records are appended to the file if you have written out any previously. When writing out Dna5, qualities are automatically taken from the sequence characters.

int writeAll(seqIO, ids, seqs[, options])

int writeAll(seqIO, ids, seqs, quals, [options])

Include Headers

seqan/seq_io.h

Parameters

seqIO	The SequenceStream object to write to. Types: SequenceStream
ids	Identifiers to write out. Types: StringSet of CharString.
seq	Sequences to write out. Types: StringSet
quals	Qualities to write out. Optional. Types: StringSet of CharString. Remarks: Qualities are ignored if the file format does not suppor them. If none are given for FASTQ, score 40 is written out for all.
options	The configuration for writing FASTA and FASTQ files. Types: SequenceOutputOptions

Return Values

An integer, 0 on success, 1 on errors.

Types: int

Member of

SequenceStream

Examples

Write out all sequences.

int main()
{
    seqan::SequenceStream seqIO("in.fasta", seqan::SequenceStream::WRITE);
    seqan::StringSet<seqan::CharString> ids;
    appendValue(ids, "seq1");
    appendValue(ids, "seq2");
    seqan::StringSet<seqan::Dna5String> seqs;
    appendValue(seqs, "CGAT");
    appendValue(seqs, "TTTT");

    int res = writeAll(seqIO, ids, seqs);
    if (res != 0)
    {
        std::cerr << "ERROR: Could not write records!\n";
        return 1;
    }

    return 0;
}

SeqAn - Sequence Analysis Library - www.seqan.de