The gto_fasta_complement replaces the ACGT bases with their complements in FASTA or Multi-FASTA file format.
For help type:
./gto_fasta_complement -h
In the following subsections, we explain the input and output paramters.
The gto_fasta_complement 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_complement [options] [[--] args]
or: ./gto_fasta_complement [options]
It replaces the ACGT bases with their complements in FASTA or Multi-FASTA file format.
-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_complement < 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
The output of the gto_fasta_complement program is FASTA or Multi-FASTA file with the ACGT base complements.
Using the input above, an output example for this is the following:
>AB000264 |acc=AB000264|descr=Homo sapiens mRNA
TGTTCTGCCGGAGGACGACGACGACGAGAGGCCCCGGTGCCGGGACCTCCCAGGTGGCGACGGGACGACGGTAACAGGG
GCCGGGGTGGATTCCTTTTCGTCGGAGGACTGAAAGGAGCGAACCCGGCTCTGTCGCTCGTATACGTCCTTCGCCGTCC
TTCACCAAACTCACCTGGAGGCCCGGGGAGTATCCTCTCCTTCGAGCCCTCCACCGGTCCGCCGTCCTTCGTCCGGTCA
CGGCGCTTAGGCGCGCGGCCCTGTCTTAGAGGACGTTTCGGGACGTCCTTGAAGAAGACCTTCTGGAAGAGGTGGGGGG
GTCGATTTTGGAGTGGGTACTTACGAGTGCGTTCAAATTAATGTCTGGACTT
>AB000263 |acc=AB000263|descr=Homo sapiens mRNA
TGTTCTACGGTAACAGGGGGCCGGAGGACGACGACGACGAGAGGCCCCGGTGCCGGTGGCGACGGGACGGGGACCTCCC
ACCGGGGTGGCCGGCTCTGTCGCTCGTATACGTCCTTCGCCGTCCTTATTCCTTTTCGTCGGAGGACTGAAAGGAGCGA
ACCACCAAACTCACCTGGAGGGTCCGGTCACGGCCCGGGGAGTATCCTCTCCTTCGAGCCCTCCACCGGTCCGCCGTCC
TTCCGCGTGGGGGGGTCGTTAGGCGCGCGGCCCTGTCTTACGGGACGTCCTTGAAGAAGACCTTCTGGAAGAGGAGGAC
GTTTATTTTGGAGTGGGTACTTACGAGTGCGTTCAAATTAATGTCTGGACTT