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