[BioRuby] Error reading ABIF SangerChromatogram data

[Naohisa GOTO]

Hi Bryan,

It may be possible that default file open mode on Windows is ASCII
and the line feed code conversion from CR+LF to LF brakes read data.

Please try the following workaround code:

    require 'bio'
    f = File.open("120605M4_05H_9.ab1", "rb")
    chromatogram_ff = Bio::Abif.open(f)
    chromatogram = chromatogram_ff.next_entry

This will be fixed in the next version: default file open mode
of Bio::FlatFile is changed to binary.

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Thu, 7 Jun 2012 14:24:36 -0500
Bryan Sibert <sibert at wisc.edu> wrote:

> Hello,
> 
> I am using BioRuby 1.4.2 on Ruby 1.9.3 installed on a 64-bit Windows Vista
> machine.  I am trying to read some .ab1 files using the BioRuby ABIF class
> which inherits SangerChromatogram.  Ruby raises a NoMethodError when I
> attempt this.  Below is a simple program based up on the example usage
> provided in the documentation:
> 
>    require 'bio'
>    chromatogram_ff = Bio::Abif.open("120605M4_05H_9.ab1")
>    chromatogram = chromatogram_ff.next_entry
> 
> This raises the following error:
> 
>    C:\...\Desktop>test
> 
> C:/Ruby193/lib/ruby/gems/1.9.1/gems/bio-1.4.2/lib/bio/db/sanger_chromatogram/abif.rb:107:in
> `get_entry_data': undefined method `match' for nil:NilClass (NoMethodError)
>         from
> C:/Ruby193/lib/ruby/gems/1.9.1/gems/bio-1.4.2/lib/bio/db/sanger_chromatogram/abif.rb:85:in
> `block in get_directory_entries'
>         from
> C:/Ruby193/lib/ruby/gems/1.9.1/gems/bio-1.4.2/lib/bio/db/sanger_chromatogram/abif.rb:77:in
> `times'
>         from
> C:/Ruby193/lib/ruby/gems/1.9.1/gems/bio-1.4.2/lib/bio/db/sanger_chromatogram/abif.rb:77:in
> `get_directory_entries'
>         from
> C:/Ruby193/lib/ruby/gems/1.9.1/gems/bio-1.4.2/lib/bio/db/sanger_chromatogram/abif.rb:42:in
> `initialize'
>         from
> C:/Ruby193/lib/ruby/gems/1.9.1/gems/bio-1.4.2/lib/bio/io/flatfile/splitter.rb:55:in
> `new'
>         from
> C:/Ruby193/lib/ruby/gems/1.9.1/gems/bio-1.4.2/lib/bio/io/flatfile/splitter.rb:55:in
> `get_parsed_entry'
>         from
> C:/Ruby193/lib/ruby/gems/1.9.1/gems/bio-1.4.2/lib/bio/io/flatfile.rb:288:in
> `next_entry'
>         from C:/.../Desktop/test.rb:3:in `<main>'
> 
> 
> I am at a loss as to how to fix this.  If you have any ideas, please let me
> know.
> 
> Thanks,
> 
> Bryan
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