The gto_genomic_dna_mutate creates a synthetic mutation of a sequence file given specific rates of mutations, deletions and additions. All these paramenters are defined by the user, and their are optional.
For help type:
./gto_genomic_dna_mutate -h
In the following subsections, we explain the input and output paramters.
The gto_genomic_dna_mutate program needs two streams for the computation, namely the input and output standard. However, optional settings can be supplied too, such as the starting point to the random generator, and the edition, deletion and insertion rates. Also, the user can choose to use the ACGTN alphabet in the synthetic mutation. The input stream is a sequence File.
The attribution is given according to:
Usage: ./gto_genomic_dna_mutate [options] [[--] args]
or: ./gto_genomic_dna_mutate [options]
Creates a synthetic mutation of a sequence file given specific rates of mutations,
deletions and additions
-h, --help show this help message and exit
Basic options
< input.seq Input sequence file (stdin)
> output.seq Output sequence file (stdout)
Optional
-s, --seed= Starting point to the random generator
-m, --mutation-rate= Defines the mutation rate (default 0.0)
-d, --deletion-rate= Defines the deletion rate (default 0.0)
-i, --insertion-rate= Defines the insertion rate (default 0.0)
-a, --ACGTN-alphabet When active, the application uses the ACGTN alphabet
Example: ./gto_genomic_dna_mutate -s -m -d -i
-a < input.seq > output.seq
An example of such an input file is:
TCTTTACTCGCGCGTTGGAGAAATACAATAGTGCGGCTCTGTCTCCTTATGAAGTCAACAATTTCGCTGGGACTTGCGGC
TCTTTACTCGCGCGTTGGAGAAATACAATAGTGCGGCTCTGTCTCCTTATGAAGTCAACAATTTCGCTGGGACTTGCGGC
GACTTCATCGTGGTCTCTGTCATTATGCGCTCCAACGCATAACTTTGCGCCAGAAGATAGATAGAATGGTGTAAGAAACT
GTAATATATATAATGAACTTCGGCGAGTCTGTGGAGTTTTTGTTGCATTAGAGAGCCAAGAGGTCGGACGTCCTCACGTA
GCCCGAGACGGGCAGGGCGATGGCGACTGAACGGGCTCCATATCACTTTGAGCTTTTATGCTTTCGACTCCTCCAGGAGC
TGAACAACCTTGTTCCCGGCAAAGCCCACTGCGTCATGGAGCTCACGGTCTACATTCATGACTGACTAACCGTAAACTGC
The output of the gto_genomic_dna_mutate program is a sequence file whith the synthetic mutation of input file.
Using the input above with the seed value as 1 and the mutation rate as 0.5, an output example for this is the following:
TCACGACTGTCGCGTTGGCACACCAGATAGGTGCTTCTACGTTTTGTATCTAATTTACAATTCTCGCTGGGAGTTCATTC
GCTATTGATGGGACTAGAAACCCATCCGTAGCTTGCCGCCGTTTAAGAATAAACACTCCACTTGCACCGAGACGTAGCGC
AACCAAGGCTATGTTCTTTGACCTTATGCGGTCCAACGCAGGAGTAGACCCCCGTAGTTAGGTACTATCGCAGAATAGGC
TTAAGCAGCCGTGCTGAACGCTGGAGGGTCTGTTTAATTACTGAGTGAATGGAGAGCTAAGAGTTCGGAGCACCGCACGA
GGCTCAAGAGCGGAAGGGCGTCAGCCTGGCGACCACCTGCCTACCGCTCGAGTCTGTCTTCACTACAGTCCGTGGAGGAC
CCCCAACGACCTAGTATCCTACAAAGCCGCATACGACTTACAGAACAGGCTGTATCGTCAGGAGTGTGTACACGAAGAGT
A