# bio-tm_hmm [![Build Status](https://secure.travis-ci.org/wwood/bioruby-sra.png)](http://travis-ci.org/#!/wwood/bioruby-tm_hmm) A bioruby plugin for running the transmembrane domain predictor TMHMM automatically on multiple sequences in a FASTA file and manipulation of the results. ## Installation ``` gem install bio-tm_hmm ``` ## Usage ``` Usage: bio-tm_hmm [-f NUM] [-g NUM] [fasta_filename] fasta file can also be piped in on STDIN. without arguments, a description of the transmembrane domains is printed out for each input sequence -f MIN_TRANSMEMBRANE_DOMAINS, Print those sequences that have at _least_ MIN_TRANSMEMBRANE_DOMAINS transmembrane domain(s). Prints out the sequences in FASTA format. --filter-in -g MAX_TRANSMEMBRANE_DOMAINS, Print those sequences that have at _most_ MAX_TRANSMEMBRANE_DOMAINS transmembrane domain(s). Prints out the sequences in FASTA format. --filter-out ``` 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 don't (converse is -g). For instance, to filter out all sequences that have less than 2 predicted transmembrane domains: ``` bio-tm_hmm -f 2