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 

Parameter order

You may write:

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


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

both will work and produce the same results.

Parameter action

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.

Multiple accession numbers

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

bio fetch NC_045512 MN996532 

Parameter forms

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

Interactive mode

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

bio convert  ATGATTATATATA --translate -i 
>1 translated

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

The coordinate system is 1 based

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

Number formatting

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:

  • 5000
  • 5,000
  • 5k or 5kb
  • 5K or 5KB