bettersam 0.0.1.alpha → 0.0.2

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 7c1a3a8ba1fafb9fce91bc76a62d3869a4c60b5e
+  data.tar.gz: 477b54306d56e399ce7a996dcd8f80ef5db44fd6
+SHA512:
+  metadata.gz: 6d8d6e1e3d2ff18fb3021a0eb4357da7de7b8d1669ed2d0313dff291bf7093d58ab006fa65d54f933af898f2cb4dc7109621a031ab5118a778902b53bd15e2c1
+  data.tar.gz: 5145d5824bbc7891e900cdddb9b80fe1de837fb28c5467a5ec2d3eb55a5402c3ff1588d56703626cef133519310993f0c8d8181f72ab217a60800f2dfb55f1ab

data/LICENSE

@@ -0,0 +1,20 @@
+The MIT License (MIT)
+
+Copyright (c) 2013 Richard Smith
+
+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

@@ -0,0 +1,16 @@
+BetterSAM
+============
+
+A SAM library for ruby, based on https://github.com/jesserod/samruby.
+
+[![Gem Version](https://badge.fury.io/rb/bettersam.png)][gem]
+[![Build Status](https://secure.travis-ci.org/Blahah/bettersam.png?branch=master)][travis]
+[![Dependency Status](https://gemnasium.com/Blahah/bettersam.png?travis)][gemnasium]
+[![Code Climate](https://codeclimate.com/github/Blahah/bettersam.png)][codeclimate]
+[![Coverage Status](https://coveralls.io/repos/Blahah/bettersam/badge.png?branch=master)][coveralls]
+
+[gem]: https://badge.fury.io/rb/bettersam
+[travis]: https://travis-ci.org/Blahah/bettersam
+[gemnasium]: https://gemnasium.com/Blahah/bettersam
+[codeclimate]: https://codeclimate.com/github/Blahah/bettersam
+[coveralls]: https://coveralls.io/r/Blahah/bettersam

data/Rakefile

@@ -0,0 +1,9 @@
+require 'rake/testtask'
+
+Rake::TestTask.new do |t|
+  t.libs << 'test'
+end
+
+desc "Run tests"
+task :default => :test
+

data/lib/bettersam.rb

@@ -19,6 +19,8 @@ class BetterSam
 
 public
   attr_accessor :name, :flag, :chrom, :pos, :mapq, :cigar, :mchrom, :mpos, :insert, :seq, :qual, :tags
+  attr_accessor :snp
+  attr_reader :cigar_list
 
   def initialize(line=nil)
     @tags = {}
@@ -121,6 +123,123 @@ public
     !self.pair_opposite_strands?
   end
 
+  # cigar parsing methods
+
+  def exact_match?
+    @cigar=="100M"
+  end
+
+  def endpos
+    if !@cigar_list
+      self.parse_cigar
+    end
+    e = @pos
+    @cigar_list.each do |h|
+      a = h.to_a
+      bases = a[0][0]
+      match = a[0][1]
+      if match =~ /[MD]/
+        e += bases
+      end
+    end
+    return e
+  end
+
+  def parse_cigar
+    str = @cigar
+    l = str.length
+    @cigar_list = []
+    while str.length>0
+      if str =~ /([0-9]+[MIDNSHPX=]+)/        
+        @cigar_list << {$1[0..-2].to_i => $1[-1]}
+        str = str.slice($1.length, l)
+      else
+        puts str
+      end
+    end
+  end
+
+  # snp storing
+
+  def contains_snp?(snp)
+    snp >= @pos and snp < self.endpos
+  end
+
+  def mark_snp(snp)
+    if self.contains_snp?(snp)
+      if !@cigar_list
+        self.parse_cigar
+      end
+      p = @pos
+      s = snp
+      @cigar_list.each do |h|
+        if p > s and s >= @pos
+          @snp = s - @pos
+        else
+          a = h.to_a
+          bases = a[0][0]
+          match = a[0][1]
+          if match == "M"
+            p += bases
+          elsif match == "I"
+            s += bases
+          elsif match == "D"
+            s -= bases
+          end
+        end
+      end
+      if p > s and s >= @pos
+        @snp = s - @pos
+      end
+    end
+    @snp
+  end
+
+  def transfer_snp(bs) # load in another bettersam object
+    if !self.read_unmapped? and !bs.read_unmapped?
+      if (self.read_reverse_strand? and bs.read_reverse_strand?) or (!self.read_reverse_strand? and !bs.read_reverse_strand?)
+        @snp = bs.snp
+      else
+      end
+    end
+  end
+
+  def put_snp # find the location of a snp on the genome
+    if @snp
+      if !@cigar_list
+        self.parse_cigar
+      end
+      s = @snp
+      p = 0
+      @cigar_list.each do |h|
+        if p > s
+          return s+@pos
+        else
+          a = h.to_a
+          bases = a[0][0]
+          match = a[0][1]
+          if match=="M"
+            p += bases
+          elsif match=="D"
+            s += bases
+          elsif match=="I"
+            s -= bases
+          end
+        end
+      end
+      if p > s
+        return s+@pos
+      end
+    else
+      puts "need to run mark_snp and transfer_snp first"
+      return nil
+    end
+    return -1
+  end
+
+  def get_base_at(p)
+    @seq[p]
+  end
 
 private
 
@@ -132,4 +251,5 @@ private
     Integer(x) rescue x
   end
 
+
 end

data/test/helper.rb

@@ -0,0 +1,16 @@
+require 'simplecov'
+require 'coveralls'
+
+SimpleCov.formatter = SimpleCov::Formatter::MultiFormatter[
+  SimpleCov::Formatter::HTMLFormatter,
+  Coveralls::SimpleCov::Formatter
+]
+SimpleCov.start
+
+require 'test/unit'
+begin; require 'turn/autorun'; rescue LoadError; end
+require 'shoulda-context'
+require 'bettersam'
+
+Turn.config.format = :pretty
+Turn.config.trace = 1

data/test/test_test.rb

@@ -0,0 +1,93 @@
+#!/usr/bin/env	ruby
+
+require 'helper'
+
+class TestBetterSam < Test::Unit::TestCase
+
+  context "BetterSam" do
+
+    setup do
+      # this is run before each test
+      @l1 = BetterSam.new("FCC00CKABXX:2:1101:10117:6470#CAGATCAT	81	nivara_3s	1572276	40	100M	=	1571527	-849	AGGATCGGGCCTCGTGAGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAACGAGCTCGACG	ZbaX^_baX\_S]_ZdYccYebeffddZdbebdadc[bdVeeeceeeddggggggggggggggggegeggdffbfefegggggggggggggggggggggg	AS:i:-24	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:1T1G3T0A91	YS:i:-5	YT:Z:DP")
+      @l2 = BetterSam.new("FCC00CKABXX:2:1101:10117:6470#CAGATCAT	81	chromosome03	1789384	24	4M5I91M	=	1788782	-697	AGGATCGGGCCTCGTGAGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAACGAGCTCGACG	ZbaX^_baX\_S]_ZdYccYebeffddZdbebdadc[bdVeeeceeeddggggggggggggggggegeggdffbfefegggggggggggggggggggggg	AS:i:-38	XN:i:0	XM:i:3	XO:i:1	XG:i:5	NM:i:8	MD:Z:0C1T6G85	YS:i:-5	YT:Z:DP")
+      @l3 = BetterSam.new("FCC00CKABXX:2:1101:19524:66398#CAGATCAT	145	chromosome03	1789377	23	4M1I2M1D93M	=	1788766	-711	GGAGGATCGGGCCTCGTGGGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAACGAGCTCGA	Bc`aaT\Y_]RLMKKMHEMV_T[Y[deaeeeaadbaaa\_feecedddddadfcegdcXdggcggggggggg`gfbecbcggggggggeggggggggggg	AS:i:-51	XN:i:0	XM:i:6	XO:i:2	XG:i:2	NM:i:8	MD:Z:2T0C2^A2T0A5G1A81	YS:i:0	YT:Z:DP")
+  	  @l4l = BetterSam.new("FCC00CKABXX:2:1101:16909:83925#CAGATCAT	145	nivara_3s	1572267	23	5M2D3M2I3M1I86M	=	1571498	-868	GTCCTCCAGGAGGATCGGGCCTCGTGAGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAAC	BBBBBB_Z`cU]^SZS][]USKV[L`ac`dedeageeefagegagffdd`egedgggedgggggggdggggggggefeeeQgeagggggggggggggggg	AS:i:-53	XN:i:0	XM:i:4	XO:i:3	XG:i:5	NM:i:9	MD:Z:2G2^TG3T5T0A81	YS:i:0	YT:Z:DP")
+	    @l4r = BetterSam.new("FCC00CKABXX:2:1101:16909:83925#CAGATCAT	145	chromosome03	1789378	23	7M4I3M5I81M	=	1788753	-716	GTCCTCCAGGAGGATCGGGCCTCGTGAGCCGACGGTGAGCGAGTTGTTGTTGTTCCATACGGGGGCGCCGGAGTTGGTGCTCCACAGCGGGCCGTTGAAC	BBBBBB_Z`cU]^SZS][]USKV[L`ac`dedeageeefagegagffdd`egedgggedgggggggdggggggggefeeeQgeagggggggggggggggg	AS:i:-59	XN:i:0	XM:i:4	XO:i:2	XG:i:9	NM:i:13	MD:Z:3A1A2T6G75	YS:i:0	YT:Z:DP")
+    end
+
+    should "be a paired read" do
+      assert @l1.read_paired?
+    end
+
+    should "be on the reverse strand" do
+      assert @l1.read_reverse_strand?
+    end
+
+    should "be the first pair" do
+      assert @l1.first_in_pair?
+    end
+
+    should "get the mappping position" do
+      assert @l1.pos == 1572276
+    end
+
+    should "get the end position" do
+      assert @l1.endpos == 1572376
+    end
+
+    should "get the end position too" do
+      assert @l2.endpos == 1789479, "this is #{@l1.endpos} but should be 1789479"
+    end
+
+    should "be exact match" do
+      assert @l1.exact_match?
+    end
+
+    should "contain snp" do
+      assert @l1.contains_snp?(1572283)
+    end
+
+    should "give A" do
+      assert @l1.get_base_at(0)=="A", "this is #{@l1.get_base_at(0)}, but should be A"
+    end
+
+    should "parse the cigar string correctly" do
+      @l3.parse_cigar
+      assert @l3.cigar_list.size == 5
+    end
+
+    should "parse another cigar string correctly" do
+      @l4l.parse_cigar
+      assert @l4l.cigar_list.size == 7
+    end
+
+    should "mark a snp" do
+      assert @l1.mark_snp(1572283)==7, "this is #{@l1.mark_snp(1572283)}, but i think it should be 7"
+    end
+
+    should "mark yet another snp" do
+      assert @l4l.mark_snp(1572283)==17, "this is #{@l4l.mark_snp(1572283)}, but i think it should be 17"
+    end
+
+    should "transfer a snp from one object to another" do
+      @l1.mark_snp(1572283)
+      @l2.transfer_snp(@l1)
+      assert @l2.snp == 7, "this is #{@l2.snp}, but i think it should be 7"
+    end
+
+    should "mark another snp" do
+      assert @l2.mark_snp(1789386)==2, "this is #{@l2.mark_snp(1789386)}, but i think it should be 3"
+    end 
+
+    should "mark a third snp" do
+      assert @l3.mark_snp(1789386)==9, "this is #{@l3.mark_snp(1789386)}, but i think it should be 9"
+    end
+
+    should "find the location of a snp on the genome" do
+      @l4l.mark_snp(1572283)
+      @l4r.transfer_snp(@l4l)
+      assert @l4r.put_snp==1789386, "this is #{@l4r.put_snp}, but I think it should be 1789386"
+    end
+
+  end
+end

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bettersam
 version: !ruby/object:Gem::Version
-  version: 0.0.1.alpha
-  prerelease: 6
+  version: 0.0.2
 platform: ruby
 authors:
 - Richard Smith
@@ -10,38 +9,112 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-09-17 00:00:00.000000000 Z
-dependencies: []
+date: 2014-05-07 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: turn
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: shoulda-context
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: coveralls
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 description: Extended SAM (Sequence Alignment/Map) file parsing
 email: rds45@cam.ac.uk
 executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- Rakefile
 - lib/bettersam.rb
+- test/test_test.rb
+- test/helper.rb
+- README.md
+- LICENSE
 homepage: https://github.com/blahah/bettersam
 licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>'
+  - - ">="
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 2.1.4
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Extended SAM file parsing
 test_files: []