write_fasta
Martin Asser Hansen edited this page Oct 2, 2015
·
6 revisions
write_fasta writes sequence from the data stream in FASTA format. However, a FASTA entry will only be written if a SEQ key and a SEQ_NAME key is present. If a SEQ key is present and not SEQ_NAME, then the Q_ID key will be used as SEQ_NAME - if such a key is found.
For more about the FASTA format:
http://en.wikipedia.org/wiki/Fasta_format
... | write_fasta [options]
[-? | --help] # Print full usage description.
[-x | --no_stream] # Do not emit records.
[-o <file> | --data_out=<file>] # Write result to file.
[-w <int> | --wrap=<int>] # Wrap sequences to a given width.
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-Z <string> | --compress=<string>] # Compress output using <gzip|bzip2>.
[-v | --verbose] # Verbose output.
Writing entries wrapped to blocks of 80 to STDOUT.
... | write_fasta -x -w 80
Writing entries to file 'test.fna'.
... | write_fasta -x -o test.fna
Write zipped entries to file 'test.fna.gz'.
... | write_fasta -x -Z gzip -o test.fna.gz
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
write_fasta is part of the Biopieces framework.