[BioRuby] reading multiple hmmpfam reports

[Naohisa GOTO]

Hi George,

The error may depend on the input data.
Showing the data file contents, hmmer version, and command-line options
may help to solve the problem.

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

On Fri, 16 Jan 2015 12:24:24 +0300
George Githinji <georgkam at gmail.com> wrote:

> Many thanks for the clarification!
> 
> There is a little bit more complain from the report class. Not sure why.
> 
> Users/george/.rbenv/versions/2.1.5/lib/ruby/gems/2.1.0/gems/bio-1.4.3.0001/lib/bio/appl/hmmer/report.rb:267:in
> `parse_header_data': undefined method `split' for nil:NilClass
> (NoMethodError)
>     from /Users/george/.rbenv/versions/2.1.5/lib/ruby/gems/2.1.0/gems/bio-1.4.3.0001/lib/bio/appl/hmmer/report.rb:165:in
> `initialize'
>     from /Users/george/.rbenv/versions/2.1.5/lib/ruby/gems/2.1.0/gems/bio-1.4.3.0001/lib/bio/appl/hmmer/report.rb:66:in
> `new'
>     from /Users/george/.rbenv/versions/2.1.5/lib/ruby/gems/2.1.0/gems/bio-1.4.3.0001/lib/bio/appl/hmmer/report.rb:66:in
> `block in reports'
>     from /Users/george/.rbenv/versions/2.1.5/lib/ruby/gems/2.1.0/gems/bio-1.4.3.0001/lib/bio/appl/hmmer/report.rb:64:in
> `each_line'
>     from /Users/george/.rbenv/versions/2.1.5/lib/ruby/gems/2.1.0/gems/bio-1.4.3.0001/lib/bio/appl/hmmer/report.rb:64:in
> `reports'
>     from /Users/george/Code/Ruby/parse_hmmpfam.rb:13:in `<main>'
> 
> 
> On Fri, Jan 16, 2015 at 11:36 AM, Naohisa GOTO
> <ngoto at gen-info.osaka-u.ac.jp> wrote:
> > Hi,
> >
> > This is caused by a bug of file load order by "require".
> >
> > A workaroud is to add the following lines on top of the script.
> >
> >  require 'bio'
> >  require 'bio/appl/hmmer'
> >  require 'bio/appl/hmmer/report'
> >
> > Naohisa Goto
> > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> >
> >
> > On Thu, 15 Jan 2015 18:43:05 +0300
> > George Githinji <georgkam at gmail.com> wrote:
> >
> >> With bioruby version 1.4.3.0001, I am not sure what is causing the no
> >> method error with this code taken from the example code.
> >>
> >> Running the code below gives a NoMethodError.
> >>
> >> undefined method `reports' for Bio::HMMER::Report:Class (NoMethodError)
> >>
> >> file = ARGV[0] # a hmmpfam text file with multiple results
> >>
> >> Bio::HMMER.reports(File.read(file)) do |report|
> >>   report.program['name']
> >>   report.parameter['HMM file']
> >>   report.query_info['Query sequence']
> >>   report.hits.each do |hit|
> >>     hit.accession
> >>     hit.description
> >>     hit.score
> >>     hit.evalue
> >>     hit.hsps.each do |hsp|
> >>       hsp.accession
> >>       hsp.domain
> >>       hsp.evalue
> >>       hsp.midline
> >>     end
> >>   end
> >> end
> >>
> >>
> >> --
> >> ---------------
> >> Sincerely
> >> George
> >> Skype: george_g2
> >> Blog: http://www.biorelated.com/
> >> Twitter: http://twitter.com/#!/george_l
> >> _______________________________________________
> >> BioRuby Project - http://www.bioruby.org/
> >> BioRuby mailing list
> >> BioRuby at mailman.open-bio.org
> >> http://mailman.open-bio.org/mailman/listinfo/bioruby
> >
> 
> 
> 
> -- 
> ---------------
> Sincerely
> George
> Skype: george_g2
> Blog: http://www.biorelated.com/
> Twitter: http://twitter.com/#!/george_l