The gto_permute_by_blocks permutates by block sequence, FASTA and Multi-FASTA files.
For help type:
./gto_ -h
In the following subsections, we explain the input and output paramters.
The gto_permute_by_blocks program needs two streams for the computation, namely the input and output standard. The input stream is a sequence, FASTA or Multi-FASTA file.
The attribution is given according to:
Usage: ./gto_permute_by_blocks [options] [[--] args]
or: ./gto_permute_by_blocks [options]
It permutates by block sequence, FASTA and Multi-FASTA files.
-h, --help show this help message and exit
Basic options
-b, --numbases= The number of bases in each block
-s, --seed= Starting point to the random generator
< input Input sequence, FASTA or Multi-FASTA file format (stdin)
> output Output sequence, FASTA or Multi-FASTA file format (stdout)
Example: ./gto_permute_by_blocks -b -s < input.fasta > output.fasta
An example of such an input file is:
>AB000264 |acc=AB000264|descr=Homo sapiens mRNA
ACAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCCTGGAGGGTCCACCGCTGCCCTGCTGCCATTGTCCCC
GGCCCCACCTAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAA
GTGGTTTGAGTGGACCTCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAGCAGGCCAGTGCC
GCGAATCCGCGCGCCGGGACAGAATCTCCTGCAAAGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCACCCCCCCAGC
TAAAACCTCACCCATGAATGCTCGCAACACGCAAGTTTAATTCGCAAGTTAGACCTGAACGGGAGGTGGCCACGCAAGTT
The output of the gto_permute_by_blocks program is a sequence, FASTA or Multi-FASTA file permuted following some parameters.
Using the input above with the base number as 80, an output example for this is the following:
GGCCCCACCTAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAA
GTGGTTTGAGTGGACCTCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAGCAGGCCAGTGCC
GCGAATCCGCGCGCCGGGACAGAATCTCCTGCAAAGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCACCCCCCCAGC
ACAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCCTGGAGGGTCCACCGCTGCCCTGCTGCCATTGTCCCC
TAAAACCTCACCCATGAATGCTCGCAACACGCAAGTTTAATTCGCAAGTTAGACCTGAACGGGAGGTGGCCACGCAAGTT