bio: 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

All commands can read the standard input

bio fetch AF086833  KJ660346 > genome.gb

or if the file ids.txt contains:

AF086833
KJ660346

you can run:

cat ids.txt | bio fetch > genome.gb

Some commands can create sequences on the fly

bio align GATCA GATTACA

or

bio fasta GATTACA --translate

Parameter order does not matter

You may write:

bio fasta --type CDS --end 10 genomes.gb

or:

cat genomes.gb | bio fasta --type CDS --end 10

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 fasta --type CDS --end 10  --translate genomes.gb

will produce the same results as:

bio fasta --translate --end 10 --type CDS  genomes.gb

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

or comma separated:

bio fetch NC_045512,MN996532

Parameter forms

You may use single or double dashes on parameters:

bio fasta genomes.gb --end 100

The command above is equivalent to:

bio fasta genomes.gb -end 100

The coordinate system is 1 based

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

bio fasta --start 10 --end 20 genomes.gb

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 fasta --start 10 --end 10 genomes.gb

Number formatting

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

bio fasta -start 1kb -end 2kb genomes.gb

accepted formats:

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