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1 Metadata-Version: 2.1
2 Name: bio
3 Version: 1.6.2
4 Summary: bio
5 Home-page: https://github.com/ialbert/bio
6 Author: Istvan Albert
7 Author-email: istvan.albert@gmail.com
8 Classifier: Programming Language :: Python :: 3
9 Classifier: License :: OSI Approved :: MIT License
10 Classifier: Operating System :: OS Independent
11 Requires-Python: >=3.7
12 Description-Content-Type: text/markdown
13 License-File: LICENSE
14 Requires-Dist: biopython >=1.80
15 Requires-Dist: requests
16 Requires-Dist: tqdm
17 Requires-Dist: mygene
18 Requires-Dist: pandas
19 Requires-Dist: pooch
20 Requires-Dist: gprofiler-official
21
22 # bio: making bioinformatics fun again
23
24 `bio` - command-line utilities to make bioinformatics explorations more enjoyable.
25
26 `bio` is a bioinformatics toy to play with.
27
28 Like LEGO pieces that match one another `bio` aims 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.
29
30 ## What does this software do?
31
32
33 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.
34
35 Even well-defined, supposedly simple tasks can take a seemingly inordinate number of complicated steps. The `bio` package is meant to solve that tedium.
36
37 ## Usage examples
38
39 # Fetch genbank data
40 bio fetch NC_045512 MN996532 > genomes.gb
41
42 # Convert the first then bases of the genomes to FASTA.
43 bio fasta genomes.gb --end 10
44
45 # Align the coding sequences for the S protein
46 bio fasta genomes.gb --gene S --protein | bio align | head
47
48 # Print the GFF record that corresponds to the coding sequence for gene S
49 bio gff genomes.gb --gene S
50
51 # Show the descendants of taxid 117565
52 bio taxon 117565 | head
53
54 # Show the lineage of a taxonomic rank.
55 bio taxon 117565 --lineage | head
56
57 # Get metadata on a viral sample
58 bio meta 11138 -H | head
59
60 # Define a sequence ontology terms
61 bio define exon
62
63 # Define a gene ontology terms
64 bio define food vacuole
65
66 ## Documentation
67
68 Detailed documentation is maintained at
69
70 * https://www.bioinfo.help/
71
72 ## Quick install
73
74 `bio` works on Linux and Mac computers and on Windows when using the Linux Subsystem.
75
76 pip install bio --upgrade
77
78 See more details in the [documentation][docs].
79
80 ## `bio` is stream oriented
81
82 `bio` supports stream oriented programming where the output of one task may be chained into the second. Take the example above
83 but now start with a file `acc.txt` that contains just the accession numbers:
84
85 NC_045512
86 MN996532
87
88 we can run `bio` to generate a VCF file with the variants of the S nucleotides forming the S protein like so:
89
90 cat acc.txt | bio fetch | bio fasta --gene S | bio align --vcf | head
91
92 to print:
93
94 ##fileformat=VCFv4.2
95 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
96 ##FILTER=<ID=PASS,Description="All filters passed">
97 ##INFO=<ID=TYPE,Number=1,Type=String,Description="Type of the variant">
98 ##contig=<ID=YP_009724390.1,length=3822,assembly=YP_009724390.1>
99 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT QHR63300.2
100 YP_009724390.1 33 33C/T C T . PASS TYPE=SNP GT 1
101 YP_009724390.1 54 54T/A T A . PASS TYPE=SNP GT 1
102 YP_009724390.1 60 60C/T C T . PASS TYPE=SNP GT 1
103 YP_009724390.1 69 69A/G A G . PASS TYPE=SNP GT 1
104
105
106 ## Who is `bio` designed for?
107
108 The software was written to teach bioinformatics and is the companion software to the [Biostar Handbook][handbook] textbook. The targeted audience comprises:
109
110 - Students learning about bioinformatics.
111 - Bioinformatics educators who need a platform to demonstrate bioinformatics concepts.
112 - Scientists working with large numbers of similar genomes (bacterial/viral strains).
113 - Scientists who need to investigate and understand the precise details of a genomic region closely.
114
115 The ideas and motivations fueling `bio` have been developed while educating the many cohorts of students who used the handbook in the classroom. `bio` is an opinionated take on how bioinformatics, particularly data representation and access, should be simplified and streamlined.
116
117 [handbook]: https://www.biostarhandbook.com/
118 [docs]: https://www.bioinfo.help/
119
120 ## Development
121
122 If you clone the repository, we recommend that you install it as a development package with:
123
124 python setup.py develop
125
126 ## Testing
127
128 `bio` can test itself, to run all tests execute:
129
130 bio test
131
132 Tests are automatically built from a shell script that mimics real-life usage scenarios.
133
134 * https://github.com/ialbert/bio/blob/master/test/usage.sh
135
136 ## Generating documentation
137
138 To generate the docs, you will need the `bookdown` package:
139
140 conda install r-bookdown r-servr
141
142 To run the docs in a browse:
143
144 make
145
146 then visit http://localhost:8000
147