read_solid

Biopiece: read_solid

Description

read_solid reads and converts SOLID entries in color space to nucleotide space.

SOLID format consits of files with lines like the below one:

1379_8_1161_F3  T30010310310130010022122330001000010    6,13,27,12,15,6,12,9,4,24,25,14,15,22,4,18,27,19,13,4,4,5,6,12,11,24,8,9,19,24,12,27,4,20,14,

The resulting Biopiece record looks like this:

REC_TYPE: SOLID
SCORE_MEAN: 13.94
SEQ: taAaCcgttACcATtTGGgagtctaTttTGgGgGtt
SEQ_CS: T30010310310130010022122330001000010
SEQ_LEN: 36
SEQ_NAME: 1379_8_1161_F3
SEQ_QUAL: 6;13;27;12;15;6;12;9;4;24;25;14;15;22;4;18;27;19;13;4;4;5;6;12;11;24;8;9;19;24;12;27;4;20;14
---

The keys explained:

• SCORE_MEAN - The mean of all the quality scores in SEQ_QUAL.
• SEQ - The sequence in nucleotide space.
• SEQ_CS - The sequence in color space.
• SEQ_LEN - Sequence length.
• SEQ_NAME - Sequence length.
• SEQ_QUAL - List of quality scores.

For more about the SOLID:

http://solid.appliedbiosystems.com/

Usage

read_solid [[options]] -i <SOLID file(s)>

Options

[-?          | --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.
[-q <uint>   | --quality=<uint>]     #  Lowercase nucleotide with quality score below this limit (min:0 max:40)  -  Default=20
[-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_solid -i test.solid               #  Read SOLID entries from file.
read_solid -i test1.solid,test2.solid  #  Read SOLID entries from files.
read_solid -i '*.solid'                #  Read SOLID entries from files.
read_solid -i test.solid -n 10         #  Read first 10 SOLID entries from file.
read_solid -i test.solid -q 10         #  Change quality score threshold to 10.

See also

write_solid

Author

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

mail@maasha.dk

August 2007

License

GNU General Public License version 2

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

Help

read_solid is part of the Biopieces framework.

http://www.biopieces.org