Package: bio
bio: making bioinformatics fun againbio- command-line utilities to make bioinformatics explorations more enjoyable.biois a bioinformatics toy to play with.Like LEGO pieces that match one anotherbioaims to provide you with commands that naturally fit together and let you express your intent with short, explicit and simple commands. It is a project in an exploratory phase, we'd welcome input and suggestions on what it should grow up into.What does this software do?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. Thebiopackage is meant to solve that tedium.Usage examples# Fetch genbank data
bio fetch NC_045512 MN996532 > genomes.gb

# Convert the first then bases of the genomes to FASTA.
bio fasta genomes.gb --end 10

# Align the coding sequences for the S protein
bio fasta genomes.gb --gene S --protein | bio align | head

# Print the GFF record that corresponds to the coding sequence for gene S
bio gff genomes.gb --gene S 

# Show the descendants of taxid 117565
bio taxon 117565 | head

# Show the lineage of a taxonomic rank.
bio taxon 117565 --lineage | head

# Get metadata on a viral sample
bio meta 11138 -H | head

# Define a sequence ontology terms
bio define exon

# Define a gene ontology terms
bio define food vacuoleDocumentationDetailed documentation is maintained athttps://www.bioinfo.help/Quick installbioworks on Linux and Mac computers and on Windows when using the Linux Subsystem.pip install bio --upgradeSee more details in thedocumentation.biois stream orientedbiosupports stream oriented programming where the output of one task may be chained into the second. Take the example above
but now start with a fileacc.txtthat contains just the accession numbers:NC_045512
MN996532we can runbioto generate a VCF file with the variants of the S nucleotides forming the S protein like so:cat acc.txt | bio fetch | bio fasta --gene S | bio align --vcf | headto print:##fileformat=VCFv4.2
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FILTER=<ID=PASS,Description="All filters passed">
##INFO=<ID=TYPE,Number=1,Type=String,Description="Type of the variant">
##contig=<ID=YP_009724390.1,length=3822,assembly=YP_009724390.1>
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  QHR63300.2
YP_009724390.1  33      33C/T   C       T       .       PASS    TYPE=SNP        GT      1
YP_009724390.1  54      54T/A   T       A       .       PASS    TYPE=SNP        GT      1
YP_009724390.1  60      60C/T   C       T       .       PASS    TYPE=SNP        GT      1
YP_009724390.1  69      69A/G   A       G       .       PASS    TYPE=SNP        GT      1Who isbiodesigned for?The software was written to teach bioinformatics and is the companion software to theBiostar Handbooktextbook. 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 fuelingbiohave been developed while educating the many cohorts of students who used the handbook in the classroom.biois an opinionated take on how bioinformatics, particularly data representation and access, should be simplified and streamlined.DevelopmentIf you clone the repository, we recommend that you install it as a development package with:python setup.py developTestingbiocan test itself, to run all tests execute:bio testTests are automatically built from a shell script that mimics real-life usage scenarios.https://github.com/ialbert/bio/blob/master/test/usage.shGenerating documentationTo generate the docs, you will need thebookdownpackage:conda install r-bookdown r-servrTo run the docs in a browse:makethen visithttp://localhost:8000