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Decompress.md

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NAF Decompression Manual

Synopsis

unnaf file.naf >file.fa - Decompress into default format (FASTQ if input NAF file contains qualities, FASTA otherwise).

unnaf file.fa.naf - Decompress into automatically named 'file.fa' (the .naf file is never deleted).

unnaf --number file.naf - Show number of sequences stored in "file.naf".

unnaf --ids file.naf >ids.txt - Extract sequence IDs (accession numbers).

unnaf --fasta file.naf >file.fa - Extract FASTA-formatted sequences (even if "file.naf" has qualities).

unnaf --fastq file.naf >file.fq - Decompress into FASTQ format (fails if "file.naf" has no qualities).

Options for specifying output type

Only one of these options should be specified:

--fasta - FASTA formatted sequences (with mask, if available).

--fastq - FASTQ format. Will fail if input has no qualities.

--sequences - One sequence per line, without names or qualities.

--seq - All sequences concatenated into one, without names, qualities, or line breaks.

--number - Number of sequences.

--title - Dataset title (if available).

--ids - List of sequence IDs.

--names - List of complete sequence names.

--lengths - List of sequence lengths.

--total-length - Total sequence length (sum of lengths).

--mask - List of mask interval lengths.

--4bit - All sequences, concatenated, in 4-bit encoding (binary data). (Only works for DNA and RNA sequences).

--part-list - List of sections of NAF file.

--sizes - Sizes of sections of NAF file.

--format - Sequence type and version of NAF format found in the input.

--charcount - Number of occurrences of each sequence character.

Other options

-o FILE - Write output to FILE.

-c - Write to standard output.

--line-length N - Divide sequences into lines of N bp, ignoring line length stored in the NAF file. Effective only for --fasta output. Line length of 0 means unlimited lines, i.e., each sequence printed in single line.

--no-mask - Ignore mask, useful only for --fasta, --sequences and --seq outputs. Supported only for DNA and RNA sequences.

--binary-stderr - Set stderr stream to binary mode. Mainly useful for running test suite on Windows.

--binary-stdout - Set stdout stream to binary mode. Useful for piping decompressed sequences to md5sum on Windows.

--binary - Shortcut for --binary-stdout --binary-stderr.

-h, --help - Show usage help.

-V, --version - Show version.