General tips

Substantial effort has been devoted to making the command line more error-tolerant and user friendly.

See the help

Each command, when invoked with no parameters, will produce help:

bio --align

Use the -v flag to produce verbose outputs for each command.

You may write:

bio convert ncov --fasta --type CDS --end 10

or:

bio convert --type CDS --end 10 --fasta ncov

both will work and produce the same results.

Each parameter will be applied sequentially in an internally determined order that makes the most sense:

bio convert ncov --fasta --type CDS --end 10  --translate

will produce the same results as:

bio convert ncov --fasta --translate --end 10 --type CDS

Both commands first select CDS types, apply a slice on each sequence, and then use the translation operator.

Many commands allow using multiple accession numbers; in that case, the operations will take place sequentially on each.

bio fetch NC_045512 MN996532

You may use single or double dashes on parameters:

bio ncov --fasta --end 100

The command above is equivalent to:

bio convert ncov -fasta -end 100

Passing the -i flag allows data to be passed from the command line. For example:

bio convert  ATGATTATATATA --translate -i

>1 translated
MIIY

Note how the input was read as parameters from the command line. We make use of this feature when explicitly exploring simple data.

Coordinates are one based (inclusive on both ends) identical to GFF coordinate formats.

bio convert ncov -fasta -start 10 --end 20

The interval of 10 to 20 is 11 bases long! To make a single base long slice start and end on the same value:

bio convert ncov -fasta -start 10 --end 10

Numbers for start and end coordinates may be written in human-friendly forms, like so:

bio convert ncov -fasta -start 1kb --end 2kb

accepted formats: