Program gto_fasta_extract_pattern_coords

The gto_fasta_extract_pattern_coords extracts the header and coordinates from a Multi-FASTA file format given a pattern/motif in the sequence.

For help type:

./gto_fasta_extract_pattern_coords -h


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

Input parameters

The gto_fasta_extract_pattern_coords program needs two streams for the computation, namely the input and output standard. The input stream is a Multi-FASTA file.

The attribution is given according to:

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

It extracts the header and coordinates from a Multi-FASTA file format given a
pattern/motif in the sequence.

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

Basic options
-p, --pattern= Pattern to search in the file header
< input.fasta Input Multi-FASTA file format (stdin)
> output.coords Output coordinates (stdout)

Example: ./gto_fasta_extract_pattern_coords -p < input.fasta > output.coords


An example of such an input file is:

>AB000264 |acc=AB000264|descr=Homo sapiens mRNA
ACAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCCTGGAGGGTCCACCGCTGCCCTGCTGCCATTGTCCCC
GGCCCCACCTAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAA
GTGGTTTGAGTGGACCTCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAGCAGGCCAGTGCC
GCGAATCCGCGCGCCGGGACAGAATCTCCTGCAAAGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCACCCCCCCAGC
TAAAACCTCACCCATGAATGCTCGCAACACGCAAGTTTAATTCGCAAGTTAGACCTGAACGGGAGGTGGCCACGCAAGTT


Output

The output of the gto_fasta_extract_pattern_coords program is a Multi-FASTA file.

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

1 3 >AB000264 |acc=AB000264|descr=Homo sapiens mRNA
131 133 >AB000264 |acc=AB000264|descr=Homo sapiens mRNA
259 261 >AB000264 |acc=AB000264|descr=Homo sapiens mRNA
347 349 >AB000264 |acc=AB000264|descr=Homo sapiens mRNA