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
Print more information
Use the -v
flag to produce verbose outputs for each command.
Parameter order
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.
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
MIIY
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
or5kb
5K
or5KB