The gto_genomic_complement replaces the ACGT bases with their complements in a DNA sequence. It works in sequence file formats.
For help type:
./gto_genomic_complement -h
In the following subsections, we explain the input and output paramters.
The gto_genomic_complement program needs two paramenters, namely the input and output standard. The input stream is a sequence file.
The attribution is given according to:
Usage: ./gto_genomic_complement [options] [[--] args]
or: ./gto_genomic_complement [options]
It replaces the ACGT bases with their complements in a DNA sequence.
It works in sequence file formats
-h, --help Show this help message and exit
Basic options
< input.seq Input sequence file (stdin)
> output.seq Output sequence file (stdout)
Example: ./gto_genomic_complement < input.seq > output.seq
An example of such an input file is:
TCTTTACTCGCGCGTTGGAGAAATACAATAGTGCGGCTCTGTCTCCTTATGAAGTCAACAATTTCGCTGGGACTTGCGG
CTCTTTACTCGCGCGTTGGAGAAATACAATAGTGCGGCTCTGTCTCCTTATGAAGTCAACAATTTCGCTGGGACTTGCG
GCGACTTCATCGTGGTCTCTGTCATTATGCGCTCCAACGCATAACTTTGCGCCAGAAGATAGATAGAATGGTGTAAGAA
ACTGTAATATATATAATGAACTTCGGCGAGTCTGTGGAGTTTTTGTTGCATTAGAGAGCCAAGAGGTCGGACGTCCTCA
CGTAGCCCGAGACGGGCAGGGCGATGGCGACTGAACGGGCTCCATATCACTTTGAGCTTTTATGCTTTCGACTCCTCCA
GGAGCTGAACAACCTTGTTCCCGGCAAAGCCCACTGCGTCATGGAGCTCACGGTCTACATTCATGACTGACTAACCGTA
AACTGC
The output of the gto_genomic_complement program is a group sequence with the ACGT base complements.
Using the input above, an output example for this is the following:
AGAAATGAGCGCGCAACCTCTTTATGTTATCACGCCGAGACAGAGGAATACTTCAGTTGTTAAAGCGACCCTGAACGCC
GAGAAATGAGCGCGCAACCTCTTTATGTTATCACGCCGAGACAGAGGAATACTTCAGTTGTTAAAGCGACCCTGAACGC
CGCTGAAGTAGCACCAGAGACAGTAATACGCGAGGTTGCGTATTGAAACGCGGTCTTCTATCTATCTTACCACATTCTT
TGACATTATATATATTACTTGAAGCCGCTCAGACACCTCAAAAACAACGTAATCTCTCGGTTCTCCAGCCTGCAGGAGT
GCATCGGGCTCTGCCCGTCCCGCTACCGCTGACTTGCCCGAGGTATAGTGAAACTCGAAAATACGAAAGCTGAGGAGGT
CCTCGACTTGTTGGAACAAGGGCCGTTTCGGGTGACGCAGTACCTCGAGTGCCAGATGTAAGTACTGACTGATTGGCAT
TTGACG