pasv_lib 0.4.1 → 0.5.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/pasv_lib.rb

@@ -1,6 +1,8 @@
 require "pasv_lib/error"
 require "pasv_lib/alignment"
+require "pasv_lib/io"
 require "pasv_lib/version"
+
 require File.join __dir__, "..", "vendor", "systemu"
 
 module PasvLib

data/lib/pasv_lib/error.rb

@@ -1,3 +1,4 @@
 module PasvLib
   class Error < StandardError; end
+  class ParseError < Error; end
 end

data/lib/pasv_lib/io.rb

@@ -0,0 +1,50 @@
+require "parse_fasta"
+
+module PasvLib
+  module Io
+    def read_refs fname
+      refs = {}
+
+      ParseFasta::SeqFile.open(fname).each_record do |rec|
+        if has_gaps? rec.seq
+          raise PasvLib::ParseError,
+                "Record '#{rec.header}' had gaps!  Did you accidentally " \
+                "provide aligned sequences?"
+        end
+
+        if refs.count.zero?
+          head = "first_pasv_ref"
+        else
+          head = "pasv_ref___#{rec.id}"
+        end
+
+        refs[head] = rec.seq
+      end
+
+      refs
+    end
+
+    def read_queries fname
+      queries = {}
+
+      ParseFasta::SeqFile.open(fname).each_record do |rec|
+        if has_gaps? rec.seq
+          raise PasvLib::ParseError,
+                "Record '#{rec.header}' had gaps!  Did you accidentally " \
+                "provide aligned sequences?"
+        end
+
+        header          = "pasv_query___#{rec.header}"
+        queries[header] = rec.seq
+      end
+
+      queries
+    end
+
+    private
+
+    def has_gaps? seq
+      seq.include?("-") || seq.include?(".")
+    end
+  end
+end

data/lib/pasv_lib/version.rb

@@ -1,3 +1,3 @@
 module PasvLib
-  VERSION = "0.4.1"
+  VERSION = "0.5.0"
 end

data/pasv_lib.gemspec

@@ -25,4 +25,5 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency "rspec", "~> 3.0"
 
   spec.add_runtime_dependency "blosum", "~> 0.1.0"
+  spec.add_runtime_dependency "parse_fasta", "~> 2.5.2"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: pasv_lib
 version: !ruby/object:Gem::Version
-  version: 0.4.1
+  version: 0.5.0
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2019-10-17 00:00:00.000000000 Z
+date: 2020-05-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -66,6 +66,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 0.1.0
+- !ruby/object:Gem::Dependency
+  name: parse_fasta
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.5.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.5.2
 description: 
 email:
 - moorer@udel.edu
@@ -85,6 +99,7 @@ files:
 - lib/pasv_lib.rb
 - lib/pasv_lib/alignment.rb
 - lib/pasv_lib/error.rb
+- lib/pasv_lib/io.rb
 - lib/pasv_lib/version.rb
 - pasv_lib.gemspec
 - vendor/systemu.rb