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scores_to_dec
scores_to_dec converts ASCII encoded quality scores to decimal values depending on a specifed ASCII base value. The SCORES are encoded as ranges of ASCII characters from '!' to 'I' for base 33 or from '@' to 'h' for base 64, both ranges indicating scores from 0 to 40. The semi-colon seperated decimal values are used to substitute the value to SCORES.
Read more here:
http://en.wikipedia.org/wiki/FASTQ_format
... | scores_to_dec [options]
[-? | --help] # Print full usage description.
[-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.
Consider the following FASTQ entry in the file test.fq:
@HWI-EAS157_20FFGAAXX:2:1:888:434
TTGGTCGCTCGCTCCGCGACCTCAGATCAGACGTGGGCGAT
+HWI-EAS157_20FFGAAXX:2:1:888:434
@ABCDEFGHIJKLMNOPQRSTUVWhgfedcba`_^]\[ZYX
We can read in these sequence using read_fastq and then soft mask the sequence with scores_to_dec like this:
read_fastq -i test.fq | scores_to_dec
SCORES: 0;1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;23;40;39;38;37;36;35;34;33;32;31;30;29;28;27;26;25;24
SEQ: TTGGTCGCTCGCTCCGCGACCTCAGATCAGACGTGGGCGAT
SEQ_LEN: 41
SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:888:434
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Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2010
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
scores_to_dec is part of the Biopieces framework.