Program gto_fasta_rand_extra_chars

The gto_fasta_rand_extra_chars substitues in the DNA sequence the outside ACGT chars by random ACGT symbols. It works both in FASTA and Multi-FASTA file formats.

For help type:

./gto_fasta_rand_extra_chars -h


In the following subsections, we explain the input and output paramters.

Input parameters

The gto_fasta_rand_extra_chars program needs two streams for the computation, namely the input and output standard. The input stream is a FASTA or Multi-FASTA file.

The attribution is given according to:

Usage: ./gto_fasta_rand_extra_chars [options] [[--] args]
or: ./gto_fasta_rand_extra_chars [options]

It substitues in the DNA sequence the outside ACGT chars by random ACGT symbols.
It works both in FASTA and Multi-FASTA file formats


-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)

Example: ./gto_fasta_rand_extra_chars < input.mfasta > output.mfasta


An example of such an input file is:

>AB000264 |acc=AB000264|descr=Homo sapiens mRNA
ANAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGNCCCTGGAGGGTCCNCCGCTGCCCTGCTGCCATTGNCNCC
NGCCCCACCTAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGGCCGAGACAGCGAGCATATGCNGGAAGCGGCAGGAA
GNGGTTTGAGTGGACCTCCNGGCCCCTCATAGGAGAGGAAGCNNGGGAGGTGGCCAGGCGGCAGGAAGCAGGCCAGTGNC
GCGAATCCGNGCGCCGGGACAGAATCTCCTGCAAAGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCACCCCCCCNNN
TAAANNNTCACCCATGAATGCTCACGCAANTTTAATTACAGACCTGAA
>AB000263 |acc=AB000263|descr=Homo sapiens mRNA
GCGAATCCGNGCGCCGGGACAGAATCTCCTTCTCCACCCCCCCNNNTGCAAAGCCCTGCAGGAACTTCTTCTGGAAGACC
NGCCCCACCTAAGGAAAAGCAGCCTCCAGGAACTGACTTTCCTCGCTTGGGCCGAGACAGCGAGCATATGCNGGAAGCGG
ANAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGNCCCTGGCNCCAGGGTCCNCCGCTGCCCTGCTGCCATTGN
GAGGAAGCNNGGGAGGTGGCCAGGCGGCAGGAAGCAGGCCAGTGNCGNGGTTTGAGTGGACCTCCNGGCCCCTCATAGGA
TCACGCAANTTTAATTACAGACCTGAATAAANNNTCACCCATGAATGC


Output

The output of the gto_fasta_rand_extra_chars program is a FASTA or Multi-FASTA file.

Using the input above, an output example for this is the following:

>AB000264 |acc=AB000264|descr=Homo sapiens mRNA
ATAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCCTGGAGGGTCCCCCGCTGCCCTGCTGCCATTGTCCCC
TGCCCCACCTAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGGCCGAGACAGCGAGCATATGCGGGAAGCGGCAGGAA
GAGGTTTGAGTGGACCTCCCGGCCCCTCATAGGAGAGGAAGCCGGGGAGGTGGCCAGGCGGCAGGAAGCAGGCCAGTGTC
GCGAATCCGGGCGCCGGGACAGAATCTCCTGCAAAGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCACCCCCCCTTG
TAAAAGATCACCCATGAATGCTCACGCAAATTTAATTACAGACCTGAA
>AB000263 |acc=AB000263|descr=Homo sapiens mRNA
GCGAATCCGTGCGCCGGGACAGAATCTCCTTCTCCACCCCCCCATCTGCAAAGCCCTGCAGGAACTTCTTCTGGAAGACC
GGCCCCACCTAAGGAAAAGCAGCCTCCAGGAACTGACTTTCCTCGCTTGGGCCGAGACAGCGAGCATATGCGGGAAGCGG
AGAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGTCCCTGGCTCCAGGGTCCTCCGCTGCCCTGCTGCCATTGC
GAGGAAGCGGGGGAGGTGGCCAGGCGGCAGGAAGCAGGCCAGTGGCGCGGTTTGAGTGGACCTCCTGGCCCCTCATAGGA
TCACGCAACTTTAATTACAGACCTGAATAAAATGTCACCCATGAATGC