----------------------------------------------------------------------------------------------------------------------------------
DESCRIPTION
----------------------------------------------------------------------------------------------------------------------------------
This archive contains only the command-line TM classification module of TMSOC webserver. It does not include the 
TM predictor module. The command-line TMSOC can be executed as long as the associated TM segments of the sequences 
are provided. Note that command-line TMSOC can handle more than one input sequence.

----------------------------------------------------------------------------------------------------------------------------------
CONTENTS OF ARCHIVE
----------------------------------------------------------------------------------------------------------------------------------
PERL script:	TMSOC.pl

PERL modules:	generateTMclassification.pm computeZscore.pm computeSeqAAEntropyGrpIVL.pm computeSeqAAHydrophobicity.pm 
		computeSummaryStatistics.pm getAAHydrophobicity.pm

Sample data:	inputseq.fasta TMsegments.txt

----------------------------------------------------------------------------------------------------------------------------------
USAGE
----------------------------------------------------------------------------------------------------------------------------------
To use the command-line TMSOC, users should first decompress the file to a folder. At the command prompt, users 
should type : perl TMSOC.pl inputseq.fasta TMsegments.txt

For the input files, the sequences should be in FASTA format (see "inputseq.fasta") while the corresponding TM segments
follow the format in "TMsegments.txt".

For the output, users should expect the (1) TM classification summary and (2) masked sequence (if any exists) to be 
displayed on screen. 

To show only the masked sequences, users can execute command-line TMSOC with a '-m' option : 
perl TMSOC.pl inputseq.fasta TMsegments.txt -m

----------------------------------------------------------------------------------------------------------------------------------