bio-bigbio 0.1.3 → 0.1.4

data/README.md

@@ -33,8 +33,15 @@ fasta.each do | rec |
 end
 ```
 
-Write a FASTA file. Any object can be passed in, as long
-as it responds to 'descr' and 'seq.to_s', or 'id' and 'seq.to_s'. E.g.
+Write a FASTA file. The simple way
+
+```ruby
+fasta = FastaWriter.new(fn)
+fasta.write('Test',"agtcta")
+```
+
+Any object can be passed in, however, as long as it responds to
+'descr' and 'seq.to_s', or 'id' and 'seq.to_s'. E.g.
 
 ```ruby
 class StorageObject
@@ -46,7 +53,7 @@ mysequence.descr = 'Test'
 mysequence.seq = "agtcta"
 ```
 
-now we can write a FASTA file
+write the FASTA file
 
 ```ruby
 fasta = FastaWriter.new(fn)

data/VERSION

@@ -1 +1 @@
-0.1.3
+0.1.4

data/bio-bigbio.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-bigbio"
-  s.version = "0.1.3"
+  s.version = "0.1.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Pjotr Prins"]

data/lib/bigbio/db/fasta/fastawriter.rb

@@ -7,15 +7,21 @@ class FastaWriter
     @f = File.open(fn,"w")
   end
 
-  # write a FASTA item. An itex should respond to descr and seq,
-  # or id and seq
-  def write item
-    if item.respond_to?(:descr)
-      @f.write ">"+item.descr+"\n"
+  # write a FASTA item. Normally write using id,seq. If only one item is
+  # passed in, the item should respond to descr and seq, or id and seq. 
+  def write id, seq = nil
+    if seq == nil
+      item = id
+      if item.respond_to?(:descr)
+        @f.write ">"+item.descr+"\n"
+      else
+        @f.write ">"+item.id+"\n"
+      end
+      @f.write item.seq.to_s.strip+"\n"
     else
-      @f.write ">"+item.id+"\n"
+      @f.write ">"+id+"\n"
+      @f.write seq.to_s.strip+"\n"
     end
-    @f.write item.seq.to_s.strip+"\n"
   end
 
   def close

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-bigbio
 version: !ruby/object:Gem::Version
-  version: 0.1.3
+  version: 0.1.4
   prerelease: 
 platform: ruby
 authors:
@@ -13,7 +13,7 @@ date: 2012-02-03 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &13483940 !ruby/object:Gem::Requirement
+  requirement: &15446660 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: 1.4.1
   type: :runtime
   prerelease: false
-  version_requirements: *13483940
+  version_requirements: *15446660
 - !ruby/object:Gem::Dependency
   name: bio-logger
-  requirement: &13483220 !ruby/object:Gem::Requirement
+  requirement: &15445800 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: 0.9.0
   type: :runtime
   prerelease: false
-  version_requirements: *13483220
+  version_requirements: *15445800
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &13482380 !ruby/object:Gem::Requirement
+  requirement: &15445180 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *13482380
+  version_requirements: *15445180
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &13467960 !ruby/object:Gem::Requirement
+  requirement: &15444540 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -54,10 +54,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *13467960
+  version_requirements: *15444540
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &13466160 !ruby/object:Gem::Requirement
+  requirement: &15443800 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +65,10 @@ dependencies:
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: *13466160
+  version_requirements: *15443800
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &13465220 !ruby/object:Gem::Requirement
+  requirement: &15440240 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,7 +76,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *13465220
+  version_requirements: *15440240
 description: Fasta reader, ORF emitter, sequence translation
 email: pjotr.public01@thebird.nl
 executables:
@@ -139,7 +139,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -2925433248995829761
+      hash: -2436097965031091716
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: