clip_adaptor

Biopiece: clip_adaptor

Description

clip_adaptor clips - or removes - sequences from the end of sequences in the stream based on ADAPTOR_POS_RIGHT, ADAPTOR_POS_LEFT, and ADAPTOR_LEN_LEFT keys in the sequence records. Quality scores are clipped as well if present.

Usage

... | clip_adaptor [options]

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.

Examples

Consider the following Biopiece record in the file test.stream:

SEQ_NAME: test
SEQ: GATCGATCGTacgagcagcatctgacgtatcgatcgttgattagttgctagctatgcagtctacgacgagcaTGCTAGCTAG
SEQ_LEN: 82
SCORES: @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghhgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDChhh
ADAPTOR_POS_LEFT: 0
ADAPTOR_LEN_LEFT: 10
ADAPTOR_PAT_LEFT: gatcgatcgt
ADAPTOR_POS_RIGHT: 72
ADAPTOR_LEN_RIGHT: 10
ADAPTOR_PAT_RIGHT: tgctagctag
---

When run through clip_adaptor the following entry is the result:

clip_adaptor -I test.stream

SEQ_NAME: test
SEQ: acgagcagcatctgacgtatcgatcgttgattagttgctagctatgcagtctacgacgagca
SEQ_LEN: 62
SCORES: JKLMNOPQRSTUVWXYZ[\]^_`abcdefghhgfedcba`_^]\[ZYXWVUTSRQPONMLKJ
ADAPTOR_POS_LEFT: 0
ADAPTOR_LEN_LEFT: 10
ADAPTOR_PAT_LEFT: gatcgatcgt
ADAPTOR_POS_RIGHT: 72
ADAPTOR_LEN_RIGHT: 10
ADAPTOR_PAT_RIGHT: tgctagctag
---

See also

read_fasta

find_adaptor

trim_seq

Author

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

mail@maasha.dk

April 2011

License

GNU General Public License version 2

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

Help

clip_adaptor is part of the Biopieces framework.

http://www.biopieces.org