Program gto_fasta_reverse

The gto_fasta_reverse reverses the ACGT bases order for each read in a FASTA or Multi-FASTA file format.

For help type:

./gto_fasta_reverse -h


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

Input parameters

The gto_fasta_reverse 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_reverse [options] [[--] args]
or: ./gto_fasta_reverse [options]

It reverses the ACGT bases order for each read in a FASTA or Multi-FASTA file.

-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_reverse < input.mfasta > output.mfasta


An example of such an input file is:

>AB000264 |acc=AB000264|descr=Homo sapiens mRNA
ACAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCCTGGAGGGTCCACCGCTGCCCTGCTGCCATTGTCCC
CGGCCCCACCTAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGG
AAGTGGTTTGAGTGGACCTCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAGCAGGCCAGT
GCCGCGAATCCGCGCGCCGGGACAGAATCTCCTGCAAAGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCACCCCCC
CAGCTAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAA
>AB000263 |acc=AB000263|descr=Homo sapiens mRNA
ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGCCCCTGGAGGG
TGGCCCCACCGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGCCTCCTGACTTTCCTCGCT
TGGTGGTTTGAGTGGACCTCCCAGGCCAGTGCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGG
AAGGCGCACCCCCCCAGCAATCCGCGCGCCGGGACAGAATGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCTCCTG
CAAATAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAA


Output

The output of the gto_fasta_reverse program is FASTA or Multi-FASTA file with the bases reversed and the flag ''(Reversed)'' added in the header.

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

>AB000264 |acc=AB000264|descr=Homo sapiens mRNA (Reversed)
AAGTCCAGACATTAATTTGAACGCACTCGTAAGTACCCACTCCAAAATCGACCCCCCCACCTCTTCCAGAAGGTCTTCT
TCAAGGACGTCCCGAAACGTCCTCTAAGACAGGGCCGCGCGCCTAAGCGCCGTGACCGGACGAAGGACGGCGGACCGGT
GGAGGGCTCGAAGGAGAGGATACTCCCCGGGCCTCCAGGTGAGTTTGGTGAAGGACGGCGAAGGACGTATACGAGCGAC
AGAGCCGGGTTCGCTCCTTTCAGTCCTCCGACGAAAAGGAATCCACCCCGGCCCCTGTTACCGTCGTCCCGTCGCCACC
TGGGAGGTCCCGGCACCGGGGCCTCTCGTCGTCGTCGTCCTCCGGCAGAACA
>AB000263 |acc=AB000263|descr=Homo sapiens mRNA (Reversed)
AAAGTCCAGACATTAATTTGAACGCACTCGTAAGTACCCACTCCAAAATAAACGTCCTCCTCTTCCAGAAGGTCTTCTT
CAAGGACGTCCCGTAAGACAGGGCCGCGCGCCTAACGACCCCCCCACGCGGAAGGACGGCGGACCGGTGGAGGGCTCGA
AGGAGAGGATACTCCCCGGGCCGTGACCGGACCCTCCAGGTGAGTTTGGTGGTTCGCTCCTTTCAGTCCTCCGACGAAA
AGGAATAAGGACGGCGAAGGACGTATACGAGCGACAGAGCCGGCCACCCCGGTGGGAGGTCCCCGTCCCGTCGCCACCG
GCACCGGGGCCTCTCGTCGTCGTCGTCCTCCGGCCCCCTGTTACCGTAGAACA