From 953c2b0955de421b707cb096804757b6370d7334 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 28 Sep 2012 02:54:05 +0000 Subject: [PATCH] in progress --- forester/ruby/evoruby/exe/run_phylo_pipeline.rb | 17 ++--------------- 1 file changed, 2 insertions(+), 15 deletions(-) diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb index 5f9358c..163def7 100755 --- a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb +++ b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb @@ -23,8 +23,8 @@ module Evoruby def run unless ARGV.length >= 4 && ARGV.length <= 6 - error "arguments are: + - [E-value for hmmscan, default is 20] [hmmscan option, default is --nobias]" + error "arguments are: " + + " [E-value for hmmscan, default is 20] [hmmscan option, default is --nobias]" end input = ARGV[ 0 ] @@ -54,19 +54,6 @@ module Evoruby base_name = get_base_name input - #base_name = nil - #if input.downcase.end_with?( "_ni.fasta" ) - # base_name = input[ 0 .. input.length - 10 ] - #elsif input.downcase.end_with?( ".fasta" ) - # base_name = input[ 0 .. input.length - 7 ] - #elsif input.downcase.end_with?( "_ni.fsa" ) - # base_name = input[ 0 .. input.length - 8 ] - #elsif input.downcase.end_with?( ".fsa" ) - # base_name = input[ 0 .. input.length - 5 ] - #else - # base_name = input - #end - puts "1. hmmscan:" cmd = "#{HMMSCAN} #{hmmscan_option} --domtblout #{base_name}_hmmscan_#{e_for_hmmscan.to_s} -E #{e_for_hmmscan.to_s} #{PFAM}Pfam-A.hmm #{input}" run_command( cmd ) -- 1.7.10.2