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pyelton / Synteny-based-annotator

This collection of scripts will provide annotations for hypothetical proteins and poorly-annotated prokaryotic genes. If you are a microbiologist with a newly sequenced genome, I highly recommend this script. The citation for the paper on the method development can be found here: Yelton, A.P., Thomas B.C., Simmons, S.L., Wilmes P., Zemla A., Thelen M.P., Justice N., Banfield J.F. A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes. PLoS Computational Biology. In press.
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some problems about ruby #2

Open zhuxiaoyu123 opened 4 years ago

zhuxiaoyu123 commented 4 years ago

When i run your script, the system always notice me "/usr/local/lib/site_ruby/2.5.0/rubygems/core_ext/kernel_require.rb:92:in require': cannot load such file -- fasta_parser (LoadError)" or "/usr/local/lib/site_ruby/2.5.0/rubygems/core_ext/kernel_require.rb:92:inrequire': cannot load such file -- annotaion_finder (LoadError)". Then i tried to execute "gem install fasta_parser/annotation_finder", but no such item was found. Really hope your repsonse.

isabelschober commented 4 years ago

Hi, I'm not the author of the scripts, but I solved this issue like this:

In synteny_finder.091311.rb in lines 3 to 6 and in blast_parser.071411.rb in line 1, add the paths to the scripts that are called.

I changed synteny_finder.091311.rb lines 3 to 6 to

require './fasta_parser' #allows usage of fasta parser require './blast_pusher.071411' require './blast_job.051909' require './blast_parser.071411'

and blast_parser.071411.rb line 1 to

require './synteny_stats.071411'

and then call synteny_finder.091311.rb from within the folder all scripts are in.

If you want to call the script from another folder, you would could add full paths in these lines.