read_stockholm

Biopiece: read_stockholm

Description

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

Usage

read_stockholm [options] -i <Stockholm file(s)>

Options

[-?          | --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.

Examples

Read in the first alignment from the Rfam.seed file:

read_stockholm -i Rfam.seed -n 1

See also

invert_align

write_align

write_fasta

Author

Martin Asser Hansen - Copyright (C) - All rights reserved.

[email protected]

August 2007

License

GNU General Public License version 2

http://www.gnu.org/copyleft/gpl.html

Help

read_stockholm is part of the Biopieces framework.

http://www.biopieces.org