PIR Site Rule Scan

This program scans a sequence for PIRSR propagation: 
For a given UniProt sequences in FASTA format and the corresponding PIRSF ID, the program will search sequence
against the corresponding PIRSR models using hmmsearch. If match, the program will generate an alignment with the
corresponding template sequence using hmmalign. The output will be written as a gff file which can be used for 
PIRSR propagation. PIRSR system currently is based on HMMER2.

1) Install:
	tar zxvf SR-InterPro-20xx_yy.tar.gz  
	cd SR-InterPro-20xx_yy

2) File Structure:
   a) config.txt: The configuration file contains the following information

        # path to hmmer3 hmmsearch command
        hmmSearchCmd=/big/chenc/progs/bin/hmmsearch
        # path to hmmer3 hmmalign command
        hmmAlignCmd=/big/chenc/progs/bin/hmmalign
        # directory of site rule hmm
        srHmmDir=data/sr_hmm
        # path to site rule template sequences
        srTpSeq=data/sr_tp/sr_tp.seq
        # directory to hold temporary intermediate files
        tmpDir=./sr_tmp
        # debug flag if set to 1 then keep the intermediate files
        debug=0

   b) data/sr_hmm/*.hmm:  PIR Site Rule HMM models
   c) data/sr_tp/sr_tp.seq:   PIR Site Rule template sequences
   d) test.seq:   test.seq in FASTA format
   e) test.gff.sample:	test.seq's output in gff format
   f) sr.pl:  main program 

3) Usage:
        perl sr.pl configFile seqFile pirsfId outputGffFile

4) To Test:
        perl sr.pl conf.txt test.seq PIRSF001415 test.gff