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write_fastq
Martin Asser Hansen edited this page Oct 2, 2015
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write_fastq writes sequence from the data stream in FASTQ format if a Biopiece record contains a SEQ, SEQ_NAME, and SCORES keys.
It is possible to specify the quality score encoding base using the -e switch.
For more about the FASTQ format:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847217/
... | write_fastq [options]
[-? | --help] # Print full usage description.
[-x | --no_stream] # Do not emit records.
[-o <file> | --data_out=<file>] # Write result to file.
[-e <string> | --encoding=<string> # Encoding <base_33|base_64> - Default=base_33
[-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 to file 'test.fq'.
... | write_fastq -o test.fq -x
Writing entries using a specifed encoding with the -e switch:
... | write_fastq -e base_64 -o test.fq -x
Write zipped entries to file 'test.fq.gz'.
... | write_fastq -Z gzip -o test.fq.gz -x
Martin Asser Hansen - Copyright (C) - All rights reserved.
July 2009
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
write_fastq is part of the Biopieces framework.