[BioRuby] reading multiple hmmpfam reports
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp
Fri Jan 16 08:36:27 UTC 2015
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
> _______________________________________________
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