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read_2bit
[read_2bit] read in nucleotide sequence entries from 2bit files. The sequence is compressed using two bits per base and a table of content containing information about soft and hard masking is located at the beginning of the file.
The resulting Biopiece record consists of the following record type:
SEQ_NAME: test
SEQ_LEN: 10
SEQ: ATCGATCGAC
---
For more about the 2bit format:
http://genome.ucsc.edu/FAQ/FAQformat#format7
read_2bit [options] -i <2bit 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.
[-N | --no_mask] # Ignore soft masking.
[-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 2bit entries from a file:
read_2bit -i test.2bit
To read in only 10 records from a 2bit file:
read_2bit -n 10 -i test.2bit
To read all 2bit entries from multiple files:
read_2bit -i test1.2bit,test2.2bit
To read 2bit entries from multiple files using a glob expression:
read_2bit -i '*.2bit'
[write_2bit]
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
[read_2bit] is part of the Biopieces framework.