Program gto_fasta_info

The gto_fasta_info shows the readed information of a FASTA or Multi-FASTA file format.

For help type:


			  			./gto_fasta_info -h

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

Input parameters

The gto_fasta_info 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_info [options] [[--] args]
or: ./gto_fasta_info [options]

It shows read information of a 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              Output read information (stdout)

Example: ./gto_fasta_info < input.mfasta > output

Output example :
Number of reads      : value
Number of bases      : value
MIN of bases in read : value
MAX of bases in read : value
AVG of bases in read : value

An example of such an input file is:


			  			>AB000264 |acc=AB000264|descr=Homo sapiens mRNA
ACAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCCTGGAGGGTCCACCGCTGCCCTGCTGCCATTGTCCCC
GGCCCCACCTAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAA
GTGGTTTGAGTGGACCTCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAGCAGGCCAGTGCC
GCGAATCCGCGCGCCGGGACAGAATCTCCTGCAAAGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCACCCCCCCAGC
TAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAA
>AB000263 |acc=AB000263|descr=Homo sapiens mRNA
ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGCCCCTGGAGGGT
GGCCCCACCGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTG
GTGGTTTGAGTGGACCTCCCAGGCCAGTGCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAG
GCGCACCCCCCCAGCAATCCGCGCGCCGGGACAGAATGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCTCCTGCAAA
TAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAA

Output

The output of the gto_fasta_info program is a set of information related to the file read.

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


			  			Number of reads      : 2
Number of bases      : 736
MIN of bases in read : 368
MAX of bases in read : 368
AVG of bases in read : 368.0000