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fixup readme

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1 parent ab30617 commit 487802f9617486d73ed6eb193ab1ccec7b0bc5f5 @throwern committed May 7, 2012
Showing with 50 additions and 33 deletions.
  1. +50 −33 README.rdoc
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83 README.rdoc
@@ -13,41 +13,58 @@ This gem was modeled on the bio-samtools gem: https://github.com/helios/bioruby-
gem install bio-tabix
== Usage
-Compress the file::
- The following command will run the bgzip utility.
- You must supply input and output filenames. If you don't compress your
- data first, it will be compressed when the file is opened appending '.bgzf' to the filename.
- Bio::Tabix::TFile.compress(in_file,compressed_file)
-
-Index the file::
- Build an index by supplying the required columns.
- If you don't create an index the open method will use the default options.
- The opts parameter take a hash of index build options
- - :s => sequence/group column [1]
- - :b => beginning range column [2]
- - :e => ending range column. Can equal :b. [3]
- - :meta_char => comment character [#]
- - :line_skip => number of initial lines to ignore [0]
- tabix_file = Bio::Tabix::TFile.build_index(compressed_file, {:s => group_col, :b => pos1_col, :e => pos2_col})
-
-
-Open the file::
- Create a new TFile instance and open it.
- tabix_file = Bio::Tabix::TFile.open(compressed_file)
-
-Create a proc or lambda::
- This will be called with the value of each fileline
- my_func = lambda do |line|
- # convert text to array and print column 6
- puts line.split("\t")[6]
- end
-
-Process a region::
- Choose a group and range for your function and process it
- tabix_file.process_region('FirstGroup', 1, 500, my_func)
+=== Compress your file
+The following command will run the bgzip utility.
+You must supply input and output filenames. If you don't compress your
+data first, it will be compressed when the file is opened appending '.bgzf' to the filename.
+ Bio::Tabix::TFile.compress(in_file,compressed_file)
+
+=== Index the file
+Build an index by supplying the required columns.
+If you don't create an index the open method will use the default options.
+The opts parameter takes a hash of index build options
+- :s => sequence/group column [1]
+- :b => beginning range column [2]
+- :e => ending range column. Can equal :b [3]
+- :meta_char => comment character [#]
+- :line_skip => number of initial lines to ignore [0]
+ tabix_file = Bio::Tabix::TFile.build_index(compressed_file, {:s => group_col, :b => pos1_col, :e => pos2_col})
+
+
+=== Open your file
+Create a new TFile instance and open it.
+ tabix_file = Bio::Tabix::TFile.open(compressed_file)
+
+=== Create a proc or lambda
+This will be called with the value of each fileline
+ my_func = lambda do |line|
+ # convert text to array and print column index 3
+ puts line.split("\t")[3]
+ end
+
+=== Process a region
+Choose a group and range for your function and process it
+ tabix_file.process_region('g2', 4, 10, my_func)
+
+== Example
+=== File
+ g1 1 3 a1 b1
+ g1 2 3 a2 b2
+ g1 3 4 a3 b3
+ ...
+ g2 1 2 A1 B1
+ g2 2 4 A2 B2
+ g2 3 5 A3 B3
+ g2 4 6 A4 B4
+ ...
+
+=== Output
+ A2
+ A3
+ A4
== Dependencies:
--FFI (http://github.com/ffi/ffi)
+- FFI (http://github.com/ffi/ffi)
== Contributing to bio-tabix
* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.

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