sail

sequence analysis I/O tool

A command-line toolkit for biological sequence files. sail reads FASTA, Stockholm, and HMMER3 profile HMMs, and gives all three the same set of operations.

install

$ cargo install sail

use

A command takes a file, or - for stdin, and writes to stdout, or to the path given by -o. sail works out the format from the input; pass --format to require a particular one and fail on anything else.

$ sail count proteins.fa
$ sail names proteins.fa
$ sail grep -i kinase proteins.fa
$ sail fetch proteins.fa P01308 P01315
$ sail sort --key size -r proteins.fa -o sorted.fa
$ sail split -k 4 --prefix chunk proteins.fa

Nineteen commands in all. sail --help lists them, and each takes its own --help.

reading large files

Most commands take --read, which sets how the command walks its input:

• stream, one record at a time through a reused buffer
• memory, every record parsed up front
• indexed, a byte offset per record, read on demand
• auto, the default, which lets the command decide

sail index writes a .saidx file beside its input, holding the offset and name of every record, so a later run can address records without scanning the file again.

license

BSD-3-Clause.