read_ace
read_ace extracts reads from ACE files containing assembled reads. Padding information are currently not included, and reads overlapping the contig ends are skipped. The resulting records look like this:
STRAND: +
Q_ID: F1N2JB301C649T
ALIGN: 2:A>-,50:A>-
S_ID: contig00001
S_BEG: 19171
S_END: 19238
---
The ALIGN field contains alignment descriptors that allows you to recreate the read sequence from the original contig. Read more about this in the description of the KISS format:
http://code.google.com/p/biopieces/wiki/KissFormat
For more about the ACE format:
http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt
read_ace [options] -i <ACE file(s)>
[-? | --help] # Print full usage description.
[-i <files!> | --data_in=<files!>] # Comma separated list of files or glob expression to read.
[-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.
To read all ACE entries from a file:
read_ace -i test.ace
To read in only 10 records from a ACE file:
read_ace -n 10 -i test.ace
To read all ACE entries from multiple files:
read_ace -i test1.ace,test2.ace
To read ACE entries from multiple files using a glob expression:
read_ace -i '*.ace'
Martin Asser Hansen - Copyright (C) - All rights reserved.
December 2009
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
read_ace is part of the Biopieces framework.