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clip_seq
clip_seq clips - or removes - soft masked sequences from the beginning and end of sequences in the stream and quality scores if present.
This way of denoting what sequence requres clipping is derived from sff_extract, which is a thrid party tool in the MIRA package.
sff_extract is located in a file named mira_3rdparty... here:
http://sourceforge.net/projects/mira-assembler/files/
Read more about Mira here:
http://www.chevreux.org/projects_mira.html
... | clip_seq [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.fastq:
@GP8WFI101DE0H9
tcagTCTACGTCTCTGGACTGtaactgac
+
hhhhhhhhhhTQQOSWZ^^XMMMNNS`YY
We can read in these sequence using read_fastq and then clip the sequence with clip_seq like this:
read_fastq -i test.fq | clip_seq
SEQ_NAME: GP8WFI101DE0H9
SEQ: TCTACGTCTCTGGACTG
SEQ_LEN: 17
SCORES: hhhhhhTQQOSWZ^^XM
---
Martin Asser Hansen - Copyright (C) - All rights reserved.
October 2010
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
clip_seq is part of the Biopieces framework.