The gto_fasta_mutate creates a synthetic mutation of a FASTA file given specific rates of editions, deletions and additions. All these paramenters are defined by the user, and their are optional.
For help type:
./gto_fasta_mutate -h
In the following subsections, we explain the input and output paramters.
The gto_fasta_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 FASTA or Multi-FASTA File.
The attribution is given according to:
Usage: ./gto_fasta_mutate [options] [[--] args]
or: ./gto_fasta_mutate [options]
Creates a synthetic mutation of a fasta file given specific rates of editions,
deletions and additions
-h, --help show this help message and exit
Basic options
< input.fasta Input FASTA or Multi-FASTA file format (stdin)
> output.fasta Output FASTA or Multi-FASTA file format (stdout)
Optional
-s, --seed= Starting point to the random generator
-e, --edit-rate= Defines the edition 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_fasta_mutate -s -e -d -i
-a < input.mfasta > output.fasta
An example of such an input file is:
>AB000264 |acc=AB000264|descr=Homo sapiens mRNA
ACAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCCTGGAGGGTCCACCGCTGCCCTGCTGCCATTGTCCCC
GGCCCCACCTAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAA
GTGGTTTGAGTGGACCTCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAGCAGGCCAGTGCC
GCGAATCCGCGCGCCGGGACAGAATCTCCTGCAAAGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCACCCCCCCAGC
TAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAA
>AB000263 |acc=AB000263|descr=Homo sapiens mRNA
ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGCCCCTGGAGGGT
GGCCCCACCGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTG
GTGGTTTGAGTGGACCTCCCAGGCCAGTGCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAG
GCGCACCCCCCCAGCAATCCGCGCGCCGGGACAGAATGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCTCCTGCAAA
TAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAA
The output of the gto_fasta_mutate program is a FASTA or Multi-FASTA file whith the synthetic mutation of input file.
Using the input above with the seed value as 1 and the edition rate as 0.5, an output example for this is the following:
>AB000264 |acc=AB000264|descr=Homo sapiens mRNA
ACGCAACGNATTCCTGCTGATCATANTGTNCCGCNCCCCNGCGACGGGGNCTCNCNNGCACACATNGTACCATTGTCCAC
NCTTNCANGTNANCGCTAGCAGGCTACNGTTTNTCCTCNCCTANNCCAANCNGGCGTNNNTACACTGGCACGTGCAGGCA
TNGGTCGGCNGGNNCCTCCGGNAACGGCACCGGAGACGAAGCTCGGNGGNTATACAGGTGTCANGAAACATCCCCGCGNC
GNGTGNCCNNGAANCCANAGAGTATCTCACTCACAACCCTGCGTGCACNTCTAGAGNANGACCTTACNCACCNTCCCNTT
NNGTACCACACCAATGAACGCTGCAGAAAGTCTGTTTNNAGGNGNGCA
>AB000263 |acc=AB000263|descr=Homo sapiens mRNA
ATTTGAAGGCAANCGGNCCAGNAATNCGGNGGGTGCNGCTCNTGTNGGCTACGGNCATCGCGGCCCTGCTNTANTAAGCN
TGAACCACCGNTCGNNGCACTTAGCAATNGCGNAANCCGTCGGCACGGCGGAGACNAANCCGCTANTNNTTTCCCGCTNA
ATGGNTGTACAAGACCNACTANACCANCCTCCGTCACCACACTGGAGCGCANGATGGNNCGCTGNCTAGNAGNCNNTGAG
GCGCTCCNTCCTANAAANCCGTGGNCGAGCNCCCTATGGNAGNGTGGGGGTTTTACCGGAAGACCNTCGNGCCCTATGGG
AGCAATCANAANCTAGAAAGCTTACNGATGGTGANGAANTAGACTANG