bio-maf 0.3.2 → 1.0.0
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- data/Gemfile +3 -0
- data/README.md +34 -3
- data/bin/maf_bgzip +56 -0
- data/bin/maf_index +0 -6
- data/bio-maf.gemspec +3 -2
- data/features/bgzf.feature +62 -0
- data/features/maf-indexing.feature +10 -0
- data/features/maf-querying.feature +9 -0
- data/features/step_definitions/convert_steps.rb +1 -1
- data/features/support/env.rb +2 -0
- data/lib/bio/maf/index.rb +35 -13
- data/lib/bio/maf/maf.rb +3 -1
- data/lib/bio/maf/parser.rb +135 -39
- data/lib/bio/maf/writer.rb +4 -4
- data/man/maf_bgzip.1 +101 -0
- data/man/maf_bgzip.1.ronn +85 -0
- data/man/maf_extract.1 +5 -2
- data/man/maf_extract.1.ronn +4 -1
- data/man/maf_index.1 +3 -3
- data/man/maf_index.1.ronn +3 -2
- data/man/maf_tile.1 +5 -2
- data/man/maf_tile.1.ronn +4 -1
- data/man/maf_to_fasta.1 +1 -1
- data/spec/bio/maf/index_spec.rb +7 -0
- data/spec/bio/maf/parser_spec.rb +13 -0
- data/spec/spec_helper.rb +2 -0
- data/test/data/gap-1.kct +0 -0
- data/test/data/mm8.chrM.maf +2421 -0
- data/test/data/mm8.chrM.maf.bgz +0 -0
- data/test/data/mm8_chr7_tiny.kct +0 -0
- data/test/data/mm8_chr7_tiny.maf.gz +0 -0
- data/test/data/mm8_chrM_tiny.kct +0 -0
- metadata +31 -3
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Binary file
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data/test/data/mm8_chr7_tiny.kct
CHANGED
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Binary file
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Binary file
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data/test/data/mm8_chrM_tiny.kct
CHANGED
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Binary file
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metadata
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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name: bio-maf
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 0.
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4
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+
version: 1.0.0
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prerelease:
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platform: ruby
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authors:
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@@ -9,7 +9,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2012-
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12
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+
date: 2012-08-02 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bio-alignment
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@@ -27,6 +27,22 @@ dependencies:
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- - ~>
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- !ruby/object:Gem::Version
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version: 0.0.7
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+
- !ruby/object:Gem::Dependency
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name: bio-bgzf
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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+
- - ~>
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- !ruby/object:Gem::Version
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version: 0.2.0
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 0.2.0
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- !ruby/object:Gem::Dependency
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name: bio-genomic-interval
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requirement: !ruby/object:Gem::Requirement
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@@ -79,6 +95,7 @@ description: Multiple Alignment Format parser for BioRuby.
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email: cswh@umich.edu
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executables:
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- find_overlaps
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98
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+
- maf_bgzip
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- maf_count
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- maf_dump_blocks
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- maf_extract
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@@ -111,6 +128,7 @@ files:
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- benchmarks/sort_bench
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- benchmarks/split_bench
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- bin/find_overlaps
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- bin/maf_bgzip
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- bin/maf_count
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- bin/maf_dump_blocks
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- bin/maf_extract
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@@ -122,6 +140,7 @@ files:
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- bin/maf_write
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- bin/random_ranges
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- bio-maf.gemspec
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- features/bgzf.feature
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- features/block-joining.feature
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- features/dir-access.feature
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- features/gap-removal.feature
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@@ -159,6 +178,8 @@ files:
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- lib/bio/ucsc/genomic-interval-bin.rb
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- lib/bio/ucsc/ucsc_bin.rb
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- man/.gitignore
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- man/maf_bgzip.1
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- man/maf_bgzip.1.ronn
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- man/maf_extract.1
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- man/maf_extract.1.ronn
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- man/maf_index.1
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@@ -185,8 +206,11 @@ files:
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- test/data/gap-filled1.fa
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- test/data/gap-sp1.fa
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- test/data/gap-sp1.fa.gz
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- test/data/mm8.chrM.maf
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- test/data/mm8.chrM.maf.bgz
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- test/data/mm8_chr7_tiny.kct
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- test/data/mm8_chr7_tiny.maf
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- test/data/mm8_chr7_tiny.maf.gz
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- test/data/mm8_chr7_tiny_slice1.maf
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- test/data/mm8_chr7_tiny_slice2.maf
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- test/data/mm8_chr7_tiny_slice3.maf
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@@ -219,7 +243,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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version: '0'
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segments:
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- 0
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-
hash:
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hash: -2038588881506177726
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required_rubygems_version: !ruby/object:Gem::Requirement
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none: false
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requirements:
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@@ -233,6 +257,7 @@ signing_key:
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specification_version: 3
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summary: MAF parser for BioRuby
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test_files:
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260
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+
- features/bgzf.feature
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- features/block-joining.feature
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- features/dir-access.feature
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- features/gap-removal.feature
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@@ -274,8 +299,11 @@ test_files:
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- test/data/gap-filled1.fa
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- test/data/gap-sp1.fa
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- test/data/gap-sp1.fa.gz
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- test/data/mm8.chrM.maf
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- test/data/mm8.chrM.maf.bgz
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- test/data/mm8_chr7_tiny.kct
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- test/data/mm8_chr7_tiny.maf
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- test/data/mm8_chr7_tiny.maf.gz
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- test/data/mm8_chr7_tiny_slice1.maf
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- test/data/mm8_chr7_tiny_slice2.maf
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- test/data/mm8_chr7_tiny_slice3.maf
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