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improve doco

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1 parent ea6c3e7 commit e86ec6b9988a1466976f8ee8d285b1c2e71a768a Ben J Woodcroft committed May 3, 2012
Showing with 11 additions and 5 deletions.
  1. +7 −1 README.rdoc
  2. +4 −4 bin/bio-tm_hmm
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8 README.rdoc
@@ -14,7 +14,13 @@ Note: this software is under active development!
== Usage
- biotm_hmm -f proteome.fasta
+ bio-tm_hmm my.fasta
+
+Where my.fasta is a FASTA file with one or more protein sequences in it. Output will be a description of the transmembrane domains predicted by TMHMM.
+
+Other options include -f for printing out the fasta sequences that have some number of transmembrane domains in them, and ignoring those that done (converse is -g)
+
+ bio-tm_hmm -f 2 <my.fasta
== Developers
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8 bin/bio-tm_hmm
@@ -17,11 +17,11 @@ options = {
:filter_out => false,
}
o = OptionParser.new do |opts|
- opts.banner = [
- 'Usage: tm_hmm_wrapper.rb [-fg] [fasta_filename]',
+ opts.banner = ['',
+ 'Usage: tm_hmm_wrapper.rb [-fg] [fasta_filename]','',
"\tfasta file can also be piped in on STDIN.",
- "\twithout arguments, a description of the transmembranes is printed out for each input sequence"
- ]
+ "\twithout arguments, a description of the transmembranes is printed out for each input sequence",''
+ ].join("\n")
opts.on('-f','--filter-in [MIN_TRANSMEMBRANE_DOMAINS]','Print those sequences that have a transmembrane domain. If MIN_TRANSMEMBRANE_DOMAINS is defined, only those proteins with that many TMDs or more are printed out') do |m|
options[:filter_in] = m.to_i #gets set to 0 when optional MIN_TRANSMEMBRANE_DOMAINS is omitted
end

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