mooreryan / grep_fasta

Grep sequences from a fasta file

Grep fasta

Grep sequences from a fasta file.

Installation

Requires the Chicken Scheme compiler. If you don't have it, you can use the pre-compiled binaries.

From source

Get the source code, either with git clone or download a release.

In the main source directory, run make and optionally make install.

Usage

grep_fasta [-e] pattern seqs.fa > subset.fa

• Pass the -e flag to specify exact string matching. Else, regular expression matching is used.
• pattern is either a string for exact matching or a regular expression
• seqs.fa is a fastA file

Example

Running grep_fasta ^apple seqs.fa > subset.fa would print all sequences that start with apple in the header.