The gto_fasta_extract_read_by_pattern extracts reads from a Multi-FASTA file format given a pattern in the header. Also, this pattern is case insensitive.
For help type:
./gto_fasta_extract_read_by_pattern -h
In the following subsections, we explain the input and output paramters.
The gto_fasta_extract_read_by_pattern 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_read_by_pattern [options] [[--] args]
or: ./gto_fasta_extract_read_by_pattern [options]
It extracts reads from a Multi-FASTA file format given a pattern in the header (ID).
-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.fasta Output Multi-FASTA file format (stdout)
Example: ./gto_fasta_extract_read_by_pattern -p < input.mfasta > output.fasta
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
The output of the gto_fasta_extract_read_by_pattern program is a Multi-FASTA file.
Using the input above with the pattern value as ''264'', an output example for this is the following:
>AB000264 |acc=AB000264|descr=Homo sapiens mRNA
ACAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCCTGGAGGGTCCACCGCTGCCCTGCTGCCATTGTCCCC
GGCCCCACCTAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAA
GTGGTTTGAGTGGACCTCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAGCAGGCCAGTGCC
GCGAATCCGCGCGCCGGGACAGAATCTCCTGCAAAGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCACCCCCCCAGC
TAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAA