Program gto_fasta_extract

The gto_fasta_extract extracts sequences from a FASTA file, which the range is defined by the user in the parameters.

For help type:

./gto_fasta_extract -h

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

Input parameters

The gto_fasta_extract program needs two paramenters, which defines the begin and the end of the extraction, and two streams for the computation, namely the input and output standard. The input stream is a FASTA file.

The attribution is given according to:

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

It extracts sequences from a FASTA file.

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

Basic options
-i, --init= The first position to start the extraction (default 0)
-e, --end= The last extract position (default 100)
< input.fasta Input FASTA or Multi-FASTA file format (stdin)
> output.seq Output sequence file (stdout)

Example: ./gto_fasta_extract -i -e < input.fasta > output.seq

An example of such an input file is:

>AB000264 |acc=AB000264|descr=Homo sapiens mRNA


The output of the gto_fasta_extract program is a group sequence.

Using the input above with the value 0 as the extraction starting point and the 50 as the ending, an output example for this is the following: