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1 parent 5b8902f commit 75eb1ad37cb269449d972ad87cf55bf6e3f725b3 @pjotrp committed May 3, 2013
Showing with 5 additions and 2 deletions.
  1. +1 −0 README.md
  2. +4 −2 bin/getorf
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1 README.md
@@ -153,6 +153,7 @@ are
1. getorf: fetch all areas between start-stop and stop-stop codons in six frames (using EMBOSS when biolib is available)
2. nt2aa.rb: translate in six frames (using EMBOSS when biolib is available)
+3. fasta_filter.rb
# Install
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6 bin/getorf
@@ -7,6 +7,8 @@
#
# You can choose the heuristic on the command line (default stopstop).
+$stderr.print "WARNING: This tool has one or more known bugs! Better use the EMBOSS getorf instead for now\n"
+
rootpath = File.dirname(File.dirname(__FILE__))
$: << File.join(rootpath,'lib')
@@ -42,10 +44,10 @@ EXAMPLE
exit()
}
- opts.on("-h heuristic", String, "Heuristic (stopstop)") do | s |
+ opts.on("-h heuristic", String, "Heuristic (default #{heuristic})") do | s |
heuristic = s
end
- opts.on("-s size", "--min-size", Integer, "Minimal sequence size") do | n |
+ opts.on("-s size", "--min-size", Integer, "Minimal sequence size (default #{minsize})") do | n |
minsize = n
end
opts.on("--longest", "Only get longest ORF match") do

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