bio-twobit 0.1.3 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 13e0df3d77589aedc725b0cffa8c5362ac749990a5eef6e1c10d0d137ae8e4d3
-  data.tar.gz: 56e92c1e74b96a040cc8c22c786f2c03d1f6fac7aabb969c34e9f0e81b496055
+  metadata.gz: 54ca968d6522ecade29dea715e43dda98eff1c2ea8fff65f446dd5e5ea19b357
+  data.tar.gz: 76def4a53e2df05f421a927334bb4441de477ca77409b0e37bbd99bda79ac657
 SHA512:
-  metadata.gz: d4b7fa2a849a682739b2ae9686000adf397ad972412df8ee965feb0c165df7743a94f1f4d1b7b7d6fba0066e4b7a12b9d5fff87f5db47c7d8a76bf6bd2753456
-  data.tar.gz: 593012ebcbb5eed16157ab6990db9f6cebcb9164c2b171eff04f3e5ebc4f88360c079c118d4e064f63d7205e113a1c889c3897cfdc92a59de8915d7b57df0aeb
+  metadata.gz: ed21093a59367927ce28bc45ddba7bad0bc0d497e3516f41de9a6cc127d510a562a621ad892db9946894c48124c142cc05fcd9861adc25c649a9d32336438245
+  data.tar.gz: f0091bf42601a641c49a1de4751fc2c79f1c2059db50e2891a34738700dbc6166deaf46e0f8f16a95b506fdaf60eb2e2e2a035e1258c34c99cb4e4027f67ffc2

data/LICENSE.txt

@@ -19,3 +19,14 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 THE SOFTWARE.
+
+Code from red-datasets is used for automatic file download and caching
+https://github.com/red-data-tools/red-datasets
+
+Copyright 2017 Kouhei Sutou <kou@clear-code.com>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

@@ -13,6 +13,9 @@ Ruby bindings to [lib2bit](https://github.com/dpryan79/lib2bit) / [py2bit](https
 gem install bio-twobit
 ```
 
+Linux and macOS are supported.
+Windows is currently not supported.
+
 ## Usage
 
 Downlaod BSgenome.Hsapiens.UCSC.hg38
@@ -21,7 +24,7 @@ Downlaod BSgenome.Hsapiens.UCSC.hg38
 wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit
 ```
 
-Quick Start
+### Quick Start
 
 ```ruby
 require 'bio/twobit'
@@ -44,10 +47,19 @@ hg38.chroms.take(5)
 # ["chr3", 198295559],
 # ["chr4", 190214555],
 # ["chr5", 181538259]]
+```
+
+Fetch a sequence
 
+```ruby
 hg38.sequence("chr1", 50000, 50050)
-# "AAACAGGTTAATCGCCACGACATAGTAGTATTTAGAGTTACTAGTAAGCC"
+# "AAACAGGTTAATCGCCACGACATAGTAGTATTTAGAGTTACTAGTAAGCC" # length 50
+```
 
+* The first number is the **(0-based)** position on the chromosome/contig where the sequence should begin. 
+* The second number is the **(1-based)** position on the chromosome where the sequence should end.
+
+```ruby
 hg38.bases("chr1", 10000, 10100)
 # {"A"=>0.34, "C"=>0.49, "T"=>0.17, "G"=>0.0}
 
@@ -64,7 +76,7 @@ hg38.hard_masked_blocks("chr1", 0, 1000000)
 # [[0, 10000], [207666, 257666], [297968, 347968], [535988, 585988]]
 ```
 
-The 2-bit file must be closed explicitly. Alternatively, you can use a block. (If you forget to close the file, it will probably be closed by GC).
+The 2-bit file must be closed explicitly. Alternatively, you can use a block. Even if it is not closed, it will probably be closed by GC and there will be no problem. But this is not guaranteed.
 
 ```ruby
 # Explicitly close the file.
@@ -81,7 +93,7 @@ end
 tb.closed? # true / false
 ```
 
-If you would like to include information about soft-masked bases, you need to manually specify `masked: true`
+If you would like to include information about soft-masked bases, you need to specify `masked: true`
 
 ```ruby
 tb = Bio::TwoBit.open("test/fixtures/foo.2bit")
@@ -99,6 +111,29 @@ tb.soft_masked_blocks("chr1")
 tb.masked? # true / false
 ```
 
+## hg19, hg38, hs1...
+
+Some reference genomes are provided as classes in advance. These classes automatically download 2bit files from the UCSC site into a cache directory upon first use.
+
+```ruby
+hg19 = Bio::TwoBit::Hg19.new
+hg38 = Bio::TwoBit::Hg38.new
+hs1  = Bio::TwoBit::Hs1.new
+```
+
+Adding a new reference genome is easy. Add [here](https://github.com/ruby-on-bioc/bio-twobit/blob/main/lib/bio/twobit/references/template.erb) the id of the genome you want to use. 
+
+```
+git clone https://github.com/ruby-on-bioc/bio-twobit
+vi lib/bio/twobit/references/template.erb # Add your id to ids list.
+ruby lib/bio/twobit/references/template.erb
+rake install
+```
+
+If you want to use 2-bit files from locations other than UCSC, create your own classes [here](https://github.com/ruby-on-bioc/bio-twobit/tree/main/lib/bio/twobit/references).
+
+Pull requests are welcome.
+
 ## Development
 
 Bug reports and pull requests are welcome on GitHub at https://github.com/ruby-on-bioc/bio-twobit.
@@ -110,3 +145,6 @@ Bug reports and pull requests are welcome on GitHub at https://github.com/ruby-o
 ## License
 
 The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
+
+Code from [Red Datasets](https://github.com/red-data-tools/red-datasets) is used for automatic file download and caching. (The MIT license)
+