Program gto_genomic_count_bases

The gto_genomic_count_bases counts the number of bases in sequence, FASTA or FASTQ files.

For help type:

./gto_genomic_count_bases -h


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

Input parameters

The gto_genomic_count_bases program needs two streams for the computation, namely the input and output standard. The input stream is a sequence, FASTA or FASTQ file.

The attribution is given according to:

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

It counts the number of bases in sequence, FASTA or FASTQ files.

-h, --help Show this help message and exit

Basic options
< input Input sequence, FASTA or FASTQ file format (stdin)
> output Output read information (stdout)

Example: ./gto_genomic_count_bases < input.seq > output

Output example :
File type : value
Number of bases : value
Number of a/A : value
Number of c/C : value
Number of g/G : value
Number of t/T : value
Number of n/N : value
Number of others : value


An example of such an input file is:

TCTTTACTCGCGCGTTGGAGAAATACAATAGTGCGGCTCTGTCTCCTTATGAAGTCAACAATTTCGCTGGGACTTGCGGC
TCTTTACTCGCGCGTTGGAGAAATACAATAGTGCGGCTCTGTCTCCTTATGAAGTCAACAATTTCGCTGGGACTTGCGGC
GACTTCATCGTGGTCTCTGTCATTATGCGCTCCAACGCATAACTTTGCGCCAGAAGATAGATAGAATGGTGTAAGAAACT
GTAATATATATAATGAACTTCGGCGAGTCTGTGGAGTTTTTGTTGCATTAGAGAGCCAAGAGGTCGGACGTCCTCACGTA
GCCCGAGACGGGCAGGGCGATGGCGACTGAACGGGCTCCATATCACTTTGAGCTTTTATGCTTTCGACTCCTCCAGGAGC
TGAACAACCTTGTTCCCGGCAAAGCCCACTGCGTCATGGAGCTCACGGTCTACATTCATGACTGACTAACCGTAAACTGC


Output

The output of the gto_genomic_count_bases program is report which describes the number of each base in the file, and the file type.

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

File type : DNA
Number of bases : 480
Number of a/A : 114
Number of c/C : 116
Number of g/G : 120
Number of t/T : 130
Number of n/N : 0
Number of others : 0