Program gto_permute_by_blocks

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.

Input parameters

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


Output

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