NAME¶

fastaq_insert_or_delete_bases

DESCRIPTION¶

fastaq_insert_or_delete_bases <fasta/q in> <outfile> Deletes or inserts bases at given position(s) from a fasta/q file

positional arguments:¶

infile

Name of fasta/q file to be read

outfile

Name of output file

optional arguments:¶

-h, --help

show this help message and exit

-d Name:start:bases, --delete Name:start:bases

Delete the given bases from the given sequence. Format same as samtools view: name:start-end. This option can be used multiple times (once for each region to delete). Overlapping coords will be merged before deleting

--delete_range P,start,step

Deletes bases starting at position P in each sequence of the input file. Deletes start + (n-1)*step bases from sequence n.

-i Name:start:bases, --insert Name:start:bases

Insert a random string of bases at the given position. Format is name:position:number_to_add. Bases are added after the position. This option can be used multiple times

--insert_range P,start,step

Inserts random bases starting after position P in each sequence of the input file. Inserts start + (n-1)*step bases into sequence n.

AUTHOR¶

fastaq_insert_or_delete_bases was originally written by Martin Hunt (mh12@sanger.ac.uk)

COPYING¶

Wellcome Trust Sanger Institute Copyright © 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.