== LOG: 2010-09-26 23:30:12 Sunday  Week 39 <nanjiang@illergard>

The SCAMPI_run.pl script has been rewritten
Updates:
1. The number of input sequences is unlimited, but will be splitted into
several files if there are more than 500 sequences. This will avoid the memory
shortage problem when the xml file is too big for xslt to process. 

2. The modhmm default options changed and the detailed results are output to
the file $outpath/$basename.xml.res

3. temporary files can be saved by the --not-clean option.

Usage: mySCAMPI_run.pl [options] fasta-seq-file
Options:
    Note: input file is fasta-seq-file (labeled or non-labeled)
    --tmpdir        <dir> : set temporary directory
    --not-clean|-nc       : do not clean the temporary dir
    --modhmmopt     <str> : add modhmms option
    --outpath       <dir> : output the result to outpath
    --maxnrseq      <int> : set the maximum number of sequences in one scampi run, default=500
                          : if the fasta file contains more sequences, it will be splitted
    -scampipath     <str> : set the scampi installed path, default=/scampi
    -modhmmpath     <str> : set the modhmm installed pathpath, default=/bin

Note that the scampi installed path and modhmm installed path have to be
specified if installed at locations other than the default.

Examples: 
    ./mySCAMPI_run.pl test/test.fa --outpath out1


LOG: 2011-03-08 21:39:41 Tuesday Week 10 
A script for predicting whether proteins are TM protein or not using SCAMPI is
created, the name of the script is "isMemPro_scampi.sh"

Usage:   isMemPro_scampi.sh fasta-seq-file
  check whether proteins are TM protein or not using scampi
Options:
  -o <file>         : set outfile
  -scampipath <str> : set the scampi installed path, default=/scampi
  -modhmmpath <str> : set the modhmm installed pathpath, default=/bin
  -h|--help         : print this help message and exit
Created 2011-03-08, updated 2011-03-08, Nanjiang


It takes about 1 s to predict 1000 sequences (test/test/fa).

The output is in the format 
ID yes-or-no

yes means TM protein
no means non TM protein

Example:
$ cd test
$ ../isMemPro_scampi.sh test.fa

Output is
UniRef100_A5FX71	yes
UniRef100_Q1RAK5	yes
UniRef100_A1AC85	yes
UniRef100_B7MWC5	yes
UniRef100_A8IBG2	yes
UniRef100_C3SGD2	yes
UniRef100_B6I257	yes
UniRef100_Q328H6	yes
UniRef100_B7LLT2	yes
UniRef100_Q89MZ8	yes
...




  
