bio-bigwig 0.0.1

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data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2021 kojix2
+
+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

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+# bio-bigwig
+
+Ruby wrapper to [libBigWig](https://github.com/dpryan79/libBigWig) compatible with [pyBigWig](https://github.com/deeptools/pyBigWig).
+
+* Currently, curl does not seem to work well ((Pull requests welcome)).
+* File writing is not implemented.
+
+## Installation
+
+Installation from source.
+
+```
+git clone --recursive https://github.com/kojix2/bio-bigwig
+cd bio-bigwig
+bundle install
+bundle exec rake compile
+bundle exec rake install
+```
+
+Not yet uploaded to the Gem server.
+
+```
+gem install bio-bigwig
+```
+
+## Usage
+
+[bigWig Track Format](https://genome.ucsc.edu/goldenPath/help/bigWig.html)
+
+```ruby
+require "bio/bigwig"
+
+bw = Bio::BigWig.open("test/fixtures/test.bw")
+bw.is_bigwig?
+
+bw.chroms
+# {"1"=>195471971, "10"=>130694993}
+
+bw.chroms("1")
+# 195471971
+
+bw.header
+# {
+#           :version => 4,       the version number                        
+#            :levels => 1,       the number of zoom levels                       
+#     :bases_covered => 154,     the number of bases described                        
+#           :min_val => 0,       the minimum value                       
+#           :max_val => 2,       the maximum value                        
+#          :sum_data => 272,     the sum of all values                        
+#       :sum_squared => 500      the sum of all squared values                        
+# }
+
+bw.stats("1", 0, 3)
+# [0.2000000054637591]
+
+bw.stats("1", 0, 3, type: :max)
+# [0.30000001192092896]
+
+# types
+# mean         - the average value (default)
+# min          - the minimum value
+# max          - the maximum value
+# cov/coverage - the fraction of bases covered
+# std          - the standard deviation of the values
+# dev          - 
+# sum          - 
+
+bw.stats("1",99, 200, type: :max, nbins: 2)
+# [1.399999976158142, 1.5]
+
+bw.stats("1")
+# [1.3351851569281683]
+
+bw.values("1", 0, 3)
+# [0.10000000149011612, 0.20000000298023224, 0.30000001192092896]
+
+bw.values("1", 0, 4)
+# [0.10000000149011612, 0.20000000298023224, 0.30000001192092896, NaN]
+
+bw.intervals("1", 0, 3)
+# [[0, 1, 0.10000000149011612], [1, 2, 0.20000000298023224], [2, 3, 0.30000001192092896]]
+
+bw.intervals("1")
+# [[0, 1, 0.10000000149011612], [1, 2, 0.20000000298023224], [2, 3, 0.30000001192092896],
+# [100, 150, 1.399999976158142], [150, 151, 1.5]]
+```
+
+[bigBed Track Format](https://genome.ucsc.edu/goldenPath/help/bigBed.html)
+
+```ruby
+require "bio/bigwig"
+
+bb = Bio::BigWig.open("test/fixtures/test.bigBed")
+
+bb.entries("chr1", 10000000, 10020000) 
+# [[10009333, 10009640, "61035\t130\t-\t0.026\t0.42\t404"],                  
+#  [10014007, 10014289, "61047\t136\t-\t0.029\t0.42\t404"],                  
+#  [10014373, 10024307, "61048\t630\t-\t5.420\t0.00\t2672399"]]   
+
+bb = Bio::BigWig.open("test/fixtures/test.bigBed")
+bb.entries("chr1", 10000000, 10020000, text: false) 
+# [[10009333, 10009640],                  
+#  [10014007, 10014289],                  
+#  [10014373, 10024307]] 
+
+bb.sql
+# table RnaElements 
+# "BED6 + 3 scores for RNA Elements data "                                   
+#     (                                                                      
+#     string chrom;      "Reference sequence chromosome or scaffold"         
+#     uint   chromStart; "Start position in chromosome"                      
+#     uint   chromEnd;   "End position in chromosome"                        
+#     string name;       "Name of item"                                      
+#     uint   score;      "Normalized score from 0-1000"
+#     char[1] strand;    "+ or - or . for unknown"
+#     float level;       "Expression level such as RPKM or FPKM. Set to -1 for no data."
+#     float signif;      "Statistical significance such as IDR. Set to -1 for no data."
+#     uint score2;       "Additional measurement/count e.g. number of reads. Set to 0 for no data."
+#     )
+```
+
+## Development
+
+Pull requests are welcome!
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/kojix2/bio-bigwig.
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).