bio-gff3-pltools 0.1.0 → 0.2.0

data/README.md

@@ -1,75 +1,52 @@
-# gff3-pltools
+# bioruby-gff3-pltools
 
-[![Build Status](https://secure.travis-ci.org/mamarjan/gff3-pltools.png)](http://travis-ci.org/mamarjan/gff3-pltools)
+[![Build Status](https://secure.travis-ci.org/mamarjan/bioruby-gff3-pltools.png)](http://travis-ci.org/mamarjan/bioruby-gff3-pltools)
 
 Note: this software is under active development!
 
-This is currently an early work in progress to create parallel GFF3
-and GTF parallel tools for D and a Ruby gem which would let Ruby
-programmers use those tools from Ruby.
+This is currently an early work in progress to create a wrapper
+library for gff3-pltools.
 
 ## Installation
 
 ### Requirements
 
-The binary builds are self-contained.
-
-To build the tools from source, you'll need the DMDv2 compiler in
-your path. You can check here if there is a build of DMD available
-for your platform:
-
-  http://dlang.org/download.html
-
-Also, the rake utility is necessary to run the automated build
-scripts.
+gff3-pltools have to be installed and in the PATH. Ruby is a requirement
+too, and the rest can be installed using bundler.
 
 ### Build and install instructions
 
-Users of 32-bit and 64-bit Linux can download pre-build binary gems
-and install them using the gem command:
+Given the gff3-tools are installed, the gem command can be used to
+install the latest gem from rubygems.org:
 
 ```sh
-    gem install bio-gff3-pltools-linux32-X.Y.Z.gem
+    gem install bio-gff3-pltools
 ```
 
-Users of other plaforms can download the source package, and build
-it themselves given the DMD compiler is available for their platform.
-
-To build and install a gem for your platform, use the following steps:
+To build and install the library from source, use the following steps:
 
 ```sh
-    tar -zxvf bio-gff3-pltools-X.Y.Z.tar.gz
-    cd bio-gff3-pltools-X.Y.Z
+    tar -zxvf bioruby-gff3-pltools-X.Y.Z.tar.gz
+    cd bioruby-gff3-pltools-X.Y.Z
+    bundle install
     rake install
 ```
 
 To build a gem without installing, use the rake task "build" instead
-of install in the previous example.
-
-To build the binary tools without building a gem or a Ruby library,
-invoke the "utilities" rake task instead and copy the binaries from
-the "bin/" directory to your PATH.
+of "install" in the previous example.
 
 ### Run tests
 
-You can use the "unittests" rake task to run D unittests, like this:
-
-```sh
-    rake unittests
-```
-
-To run tests for the Ruby library, first build the D utilities and
-then start the "features" rake task, like this:
+To run cucumber tests, first make sure the  D utilities
+are available in the path and then start the "features" rake task,
+like this:
 
 ```sh
-    rake utilities
     rake features
 ```
 
 ## Usage
 
-### Ruby library
-
 To use the library in your code, after installing the gem, simply
 require the library:
 
@@ -79,165 +56,20 @@ require the library:
 
 The API docs are online:
 
-  http://mamarjan.github.com/gff3-pltools/docs/0.1.0/ruby-api/ 
+  http://mamarjan.github.com/bioruby-gff3-pltools/docs/0.2.0/ruby-api/ 
 
 For more code examples see the test files in the source tree.
 
-### gff3-ffetch utility
-
-Currently this utility supports only filtering a file, based on a
-filtering expression. For example, you can use the following command
-to filter out records with a CDS feature from a GFF3 file:
-
-```sh
-    gff3-ffetch --filter field:feature:equals:CDS path-to-file.gff3
-```
-
-The utility will use the fast (and soon parallel) D library to do the
-parsing and filtering. You can then parse the result using your
-programming language and library of choice.
-
-Currently supported predicates are "field", "attribute", "equals",
-"contains", "starts_with" and "not". You can combine them in a way
-that makes sense. First, the utility needs to know what field or
-attribute should be used for filtering. In the previous example,
-that's the "field:feature" part. Next, the utility needs to know
-what you want to do with it. In the example, that's the "equals"
-part. And then the last part in the example is a parameter to the
-"equals", which tells the utility what the attribute or field
-should be compared to.
-
-Parts of the expression are separated by a colon, ':', and if colon
-is suposed to be part of a field name or value, it can be escaped
-like this: "\\:".
-
-Valid field names are: seqname, source, feature, start, end, score,
-strand and phase.
-
-A few more examples...
-
-```sh
-    gff3-ffetch --filter attribute:ID:equals:gene1 path-to-file.gff3
-```
-
-The previous example chooses records which have the ID attribute
-with the value gene1.
-
-To see which records have no ID value, or ID which is an empty
-string, use the following command:
-
-```sh
-    gff3-ffetch --filter attribute:ID:equals: path-to-file.gff3
-```
-
-And to get records which have the ID attribute defined, you can use
-this command:
-
-```sh
-    gff3-ffetch --filter attribute:ID:not:equals: path-to-file.gff3
-```
-
-or
-
-```sh
-    gff3-ffetch --filter not:attribute:ID:equals: path-to-file.gff3
-```
-
-However, the last two commands are not completely the same. In cases
-where an attribute has multiple values, the Parent attribute for
-example, the "attribute" predicate first runs the contained predicate
-on all attribute's values and returns true when an operation
-returns true for a parent value. That is, it has an implicit "and"
-operation built-in.
-
-There are a few more options available. In the examples above, the
-data was comming from a GFF3 file which was specified on the command
-line and the output was the screen. To use the standard input as the
-source of the data, use "-" instead of a filename.
-
-The default for output is the screen, or stdout. To redirect the
-output to a file, you can use the "--output" option. Here is an
-example:
-
-```sh
-    gff3-ffetch --filter not:attribute:ID:equals: - --output tmp.gff3
-```
-
-To limit the number of records in the results, you can use the
-"--at-most" option. For example:
-
-```sh
-    gff3-ffetch --filter not:attribute:ID:equals: - --at-most 1000
-```
-
-If there are more then a 1000 records in the results, after the
-1000th record printed, a line is appended with the following content:
-"# ..." and the utility terminates.
-
-### GFF3 File validation
-
-The validation utility can be used like this:
-
-```sh
-    ./gff3-validate path/to/file.gff3
-```
-
-It will output any errors it finds to standard output. However, the
-validation utility is currently very basic, and checks only for a few
-cases: the number of columns, characters that should have been
-escaped, are the start and stop coordinates integers and if the end
-is greater then start, whether score is a float, valid values for
-strand and phase, and the format of attributes.
-
-### Benchmarking utility
-
-There is a D application for performance benchmarking.
-You can run it like this:
-
-```sh
-    ./gff3-benchmark path/to/file.gff3
-```
-
-The most basic case for the banchmarking utility is to parse the
-file into records. More functionality is available using command
-line options:
-
-```
-  -v     turn on validation
-  -r     turn on replacement of escaped characters
-  -f     merge records into features
-  -c N   feature cache size (how many features to keep in memory), default=1000
-  -l     link feature into parent-child relationships
-```
-
-Before exiting the utility prints the number of records or features
-it parsed.
-
-### Counting features
-
-The gff3-ffetch utility keeps only a small part of records in memory
-while combining them into features. To check if the cache size is
-correct, the "gff3-count-features" utility can be used to get the
-correct number of features in a file. It gets all the IDs into
-memory first, and then devises the correct number of features.
-
-To get the correct number of features in a file, use the following
-command:
-
-```sh
-    ./gff3-count-features path/to/file.gff3
-```
-
 ## Project home page
 
 Project home page can be found at the following location:
 
-  http://mamarjan.github.com/gff3-pltools/
+  http://mamarjan.github.com/bioruby-gff3-pltools/
 
 For information on the source tree, issues and
 how to contribute, see
 
-  http://github.com/mamarjan/gff3-pltools
+  http://github.com/mamarjan/bioruby-gff3-pltools
 
 The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
 

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.2.0

data/lib/bio-gff3-pltools.rb

@@ -9,4 +9,5 @@
 # In this file only require other files. Avoid other source code.
 
 require 'bio-gff3-pltools/filtering.rb'
+require 'bio-gff3-pltools/validation.rb'
 

data/lib/bio-gff3-pltools/filtering.rb

@@ -2,7 +2,8 @@ module Bio
   module PL
     module GFF3
       # Runs the gff3-ffetch utility with the specified parameters on
-      # an external file. Options include :output and :at_most.
+      # an external file. Options include :output, :at_most,
+      # :pass_fasta_through, :keep_comments, :keep_pragmas
       def self.filter_file filename, filter_string, options = {}
         if !File.exists?(filename)
           raise Exception.new("No such file - #{filename}")
@@ -16,7 +17,16 @@ module Bio
         if !options[:at_most].nil?
           at_most_option = "--at-most #{options[:at_most]}"
         end
-        gff3_ffetch = IO.popen("gff3-ffetch --filter #{filter_string} #{filename} #{output_option} #{at_most_option}")
+        if options[:pass_fasta_through]
+          fasta_option = "--pass-fasta-through"
+        end
+        if options[:keep_comments]
+          comments_option = "--keep-comments"
+        end
+        if options[:keep_pragmas]
+          pragmas_option = "--keep-pragmas"
+        end
+        gff3_ffetch = IO.popen("gff3-ffetch --filter #{filter_string} #{filename} #{output_option} #{at_most_option} #{fasta_option} #{comments_option} #{pragmas_option}")
         if output_option.nil?
           output = gff3_ffetch.read
         end
@@ -25,7 +35,8 @@ module Bio
       end
 
       # Runs the gff3-ffetch utility with the specified parameters while
-      # passing data to its stdin. Options include :output and :at_most.
+      # passing data to its stdin. Options include :output and :at_most,
+      # :pass_fasta_through, :keep_comments, :keep_pragmas
       def self.filter_data data, filter_string, options = {}
         output_option = nil
         output = nil
@@ -35,7 +46,16 @@ module Bio
         if !options[:at_most].nil?
           at_most_option = "--at-most #{options[:at_most]}"
         end
-        gff3_ffetch = IO.popen("gff3-ffetch --filter #{filter_string} - #{output_option} #{at_most_option}", "r+")
+        if options[:pass_fasta_through]
+          fasta_option = "--pass-fasta-through"
+        end
+        if options[:keep_comments]
+          comments_option = "--keep-comments"
+        end
+        if options[:keep_pragmas]
+          pragmas_option = "--keep-pragmas"
+        end
+        gff3_ffetch = IO.popen("gff3-ffetch --filter #{filter_string} - #{output_option} #{at_most_option} #{fasta_option} #{comments_option} #{pragmas_option}", "r+")
         gff3_ffetch.write data
         gff3_ffetch.close_write
         if output_option.nil?

data/lib/bio-gff3-pltools/validation.rb

@@ -0,0 +1,17 @@
+module Bio
+  module PL
+    module GFF3
+      def self.validate_file filename
+        if !File.exists?(filename)
+          raise Exception.new("No such file - #{filename}")
+        end
+
+        gff3_validate = IO.popen(["gff3-validate", "#{filename}", :err=>[:child, :out]])
+        output = gff3_validate.read
+        gff3_validate.close
+        output
+      end
+    end
+  end
+end
+

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-gff3-pltools
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-07-05 00:00:00.000000000 Z
+date: 2012-07-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
@@ -150,6 +150,7 @@ files:
 - VERSION
 - lib/bio-gff3-pltools.rb
 - lib/bio-gff3-pltools/filtering.rb
+- lib/bio-gff3-pltools/validation.rb
 - LICENSE.txt
 - README.md
 homepage: http://mamarjan.github.com/gff3-pltools/
@@ -165,6 +166,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
+      segments:
+      - 0
+      hash: -1031554001
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -178,4 +182,3 @@ signing_key:
 specification_version: 3
 summary: Ruby wrapper for the gff3-pltools.
 test_files: []
-has_rdoc: