Work in progress.
bio - command-line utilities to make bioinformatics explorations more enjoyable.
Typical usage:
bio task data1 data2 --param1 --param2
where task can be: fetch, align, convert and many others.
- Documentation: https://www.bioinfo.help/
- Usage examples: bio-examples.sh
This software is designed to teach bioinformatics concepts.
If you've ever done bioinformatics, you know how even seemingly straightforward tasks require multiple steps, arcane incantations, and various other preparations that slow down progress.
Even well-defined, supposedly simple tasks can take a seemingly inordinate number of complicated steps. The bio package is meant to solve that tedium. With bio, you can write things like this:
bio fetch NC_045512 --rename ncov
bio fetch MN996532 --rename ratg13
to fetch the data from NCBI and rename data to more meaningful labels, then write:
bio align ncov:S ratg13:S --end 60 --pep1
to align the DNA for the S protein while also showing the translation with one letter peptide code:
# Ident=57(95.0%) Mis=3(5.0%) Gaps=0(0.0%) Target=(1, 60) Query=(1, 60) Length=60 Score=273.0 NUC.4.4(11,1)
M F V F L V L L P L V S S Q C V N L T T
YP_009724390 ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACC
||||||||||||||||||||||||||||||||.||||||||||||||||||||.|||||. 60
QHR63300.2 ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTTTCTAGTCAGTGTGTTAATCTAACAACT
M F V F L V L L P L V S S Q C V N L T T
bio was designed to use words that make sense: align, translate, complement, protein, taxon, type, etc. If you wanted to align the same sequences when translated into proteins bio lets you write:
bio align ncov:S ratg13:S --end 60 --translate
to generate:
# Ident=20(100.0%) Mis=0(0.0%) Gaps=0(0.0%) Target=(1, 20) Query=(1, 20) Length=20 Score=98.0 BLOSUM62(11,1)
YP_009724390 MFVFLVLLPLVSSQCVNLTT
|||||||||||||||||||| 20
QHR63300.2 MFVFLVLLPLVSSQCVNLTT
Beyond alignments, there is a lot more to bio. We recommend looking at the documentation
The software was written to teach bioinformatics and is the companion software to the Biostar Handbook textbook. The targeted audience comprises:
- Students learning about bioinformatics.
- Bioinformatics educators who need a platform to demonstrate bioinformatics concepts.
- Scientists working with large numbers of similar genomes (bacterial/viral strains).
- Scientists who need to investigate and understand the precise details of a genomic region closely.
The ideas and motivations fueling bio have been developed while educating the many cohorts of students who used the handbook in the classroom.
You see, in bioinformatics, many tasks that should be straightforward are, instead, needlessly complicated. bio is an opinionated take on how bioinformatics, particularly data representation and access, should be simplified.
The documentation is maintained at
bio works on Linux and Mac computers and on Windows when using the Linux Subsystem.
pip install bio --upgrade
See more details in the documentation.
If you clone the repository, we recommend that you install it as a development package with:
python setup.py develop
Testing uses the pytest framework:
pip install pytest
To run all tests, use:
make test
Tests are automatically built from a test script that mimics real-life usage scenarios.
To add a new test, first run the command you wish to test, for example:
bio fetch foo --gff > output.gff
in the test/data directory. After that, add the same command above into the master script:
followed by:
make build_tests
The latter command will automatically generate a Python test for each line in the master script.
The automatically generated test will verify that the command is operational and that the output matches the expectations.
To generate the docs, you will need the bookdown package:
conda install r-bookdown r-servr
To run the docs in a browse:
make
then visit http://localhost:8000
To render the docs write:
make docs
To push out the latest docs:
make sync