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read_stockholm
Martin Asser Hansen edited this page Oct 2, 2015
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read_stockholm read in entries from Stockholm files used by Pfam and Rfam to hold sequence alignments.
For more about the Stockholm format:
http://en.wikipedia.org/wiki/Stockholm_format
read_stockholm [options] -i <Stockholm file(s)>
[-? | --help] # Print full usage description.
[-i <files!> | --data_in=<files!>] # Read input data from file.
[-n <uint> | --num=<uint>] # Limit number of records to read.
[-I <file!> | --stream_in=<file!>] # Read input stream from file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output stream to file - Default=STDOUT
[-v | --verbose] # Verbose output.
Read in the first alignment from the Rfam.seed file:
read_stockholm -i Rfam.seed -n 1
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
read_stockholm is part of the Biopieces framework.