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mutate_seq
#summary Introduce mutations into sequences in the stream.
mutate_seq introduces mutations into sequences in the stream based on either an exact number of mutations, or a percentage of the sequence length. The type of sequence is guessed and mutations are introduced at random in such a way that no two mutations can occur at the same position.
... | mutate_seq [options]
[-? | --help] # Print full usage description.
[-n <uint> | --number=<uint>] # Number of mutations to introduce.
[-p <float> | --percent=<float>] # Percentage of residues to mutate.
[-t <string> | --type=<sting>] # Sequence type (dna|rna|protein) - Default=guessed!
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
Consider the following entry in the FASTA file test.fna:
>test
ATGTGCACATTCGACTAGCA
Now, we can read this sequence with read_fasta and pipe it to mutate_seq and specify a number
of mutations to be introduced via the -n switch:
read_fasta -i test.fna | mutate_seq -n 3
SEQ: ATGTGCACACTCTACTAGCG
SEQ_NAME: test
SEQ_LEN: 20
---
We can also illustrate this by re-reading the sequence and compare the original with a sequence with 10% (using the -p switch) mutated residues using align_seq:
read_fasta -i test.fna | mutate_seq -p 10 | read_fasta -i test.fna | write_align -x
. .
test ATGTGAACATTCGAGTAGCA
||||| |||||||| |||||
test ATGTGCACATTCGACTAGCA
. .
Martin Asser Hansen - Copyright (C) - All rights reserved.
June 2009
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
mutate_seq is part of the Biopieces framework.