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write_2bit
Martin Asser Hansen edited this page Oct 2, 2015
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[write_2bit] write nucleotide sequence in 2bit format. The sequence is compressed using two bits per base and a table of content containing information about soft and hard masking is included at the beginning of the file.
For more about the 2bit format:
http://genome.ucsc.edu/FAQ/FAQformat#format7
WARNING there appear to be a bug in this program since Jim Kent's twoBitToFa segfaults trying to read files created with [write_2bit] though.
write_2bit [options]
[-? | --help] # Print full usage description.
[-x | --no_stream] # Do not emit records.
[-o <file> | --data_out=<file>] # Write result to file.
[-N | --no_mask] # Ignore soft masking.
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output stream to file - Default=STDOUT
[-v | --verbose] # Verbose output.
To write all sequence from the stream to a 2bit file, do:
... | write_2bit -o <2bit file> -x
[read_2bit]
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
[write_2bit] is part of the Biopieces framework.