SequenceStream

Building upon the more low-level sequence I/O functionality of SeqAn, this class provides easier to use I/O facilities. Especially, the underlying stream layer and using RecordReaders is hidden from the user. This is achieved by using dynamic polymorphism which comes at some performance cost.

Include Headers

seqan/seq_io.h

Remarks

Operation Mode

File Format and File Type

When reading, there are two operation modes: Normal reading and reading of "persistent" records. When reading in "persistent" mode, SequenceStream will scan over each record twice: Once for determining its size and once for actually reading the sequences. After the first pass, we can allocate a buffer of the exact size we need. This can save memory up to a factor of two, at the cost of scanning each record twice. Note that this is only possible for reading uncompressed files.

The file type determines whether a file is stored as raw text or whether it is compressed. Examples for file types are text files or gzip compressed files (FILE.gz). The file format considers the contents of the raw/decompressed file. Examples for file formats are FASTA, FASTQ, or EMBL.

When reading, the file type and format are guessed from the file itself. You do not have to specify any but you can force the SequenceStream to use the ones you provide. When writing, you should specify a file type and format when constructing the SequenceStream object. Otherwise, it will default to writing out raw-text FASTA files.

Member Functions

SequenceStream

Constructor

Functions

atEnd	Check whether a SequenceStream is at the end of the file.
close	Close the SequenceStream.
flush	Write all data from SequenceStream to disk.
isGood	Check whether a SequenceStream object is ready for reading.
open	Open or re-open a file using a SequenceStream.
readAll	Read all sequence records from a SequenceStream object.
readRecord	Read the next sequence record from SequenceStream.
writeAll	Write sequence records from to a SequenceStream object.
writeRecord	Write one sequence record from to a SequenceStream object.

Examples

Read the sequence file (FASTA or FASTQ) from argv[1] record by record. The identifiers and sequences of the stream are printed to stdout. See the documentation of readRecord, readBatch, and readAll for more examples, including record-wise reading, reading in batches, and reading all records in a file.

File "sequence_stream_read.cpp"

1	#include <seqan/basic.h>
2	#include <seqan/seq_io.h>
3	#include <seqan/sequence.h>
4
5	using namespace seqan;
6
7	// USAGE: sequence_read_stream_read FILE
8	//
9	// Print the contents of sequence FILE to stdout in tabular format.
10
11	int main(int argc, char ** argv)
12	{
13	if (argc != 2)
14	{
15	std::cerr << "USAGE: " << argv[0] << " SEQUENCE.{fa,fq}\n";
16	return 1;
17	}
18
19	SequenceStream seqStream(argv[1]);
20	if (!isGood(seqStream))
21	{
22	std::cerr << "ERROR: Could not open " << argv[1] << " for reading.\n";
23	return 1;
24	}
25
26	seqan::CharString id, seq;
27	while (!atEnd(seqStream))
28	{
29	if (readRecord(id, seq, seqStream) != 0)
30	{
31	std::cerr << "Problem reading from " << argv[1] << "\n";
32	return 1;
33	}
34	std::cout << id << "\t" << seq << "\n";
35	}
36
37	return 0;
38	}

Open a SequenceStream for writing and write two sequences to it.

File "sequence_stream_write.cpp"

1	#include <seqan/basic.h>
2	#include <seqan/seq_io.h>
3	#include <seqan/sequence.h>
4
5	using namespace seqan;
6
7	// USAGE: sequence_read_stream_write FILE
8	//
9	// Print some sequences to the file FILE
10
11	int main(int argc, char ** argv)
12	{
13	if (argc != 2)
14	{
15	std::cerr << "USAGE: " << argv[0] << " SEQUENCE.{fa,fq}\n";
16	return 1;
17	}
18
19	SequenceStream seqStream(argv[1], SequenceStream::WRITE);
20	if (!isGood(seqStream))
21	{
22	std::cerr << "ERROR: Could not open " << argv[1] << " for writing.\n";
23	return 1;
24	}
25
26	if (writeRecord(seqStream, "one", "CGAT") != 0 \|\|
27	writeRecord(seqStream, "two", "ASDF") != 0)
28	{
29	std::cerr << "ERROR: Problem writing to " << argv[1] << "\n";
30	return 1;
31	}
32
33	return 0;
34	}