#!/usr/bin/perl
# the path to your perl distribution may be different
# to determine the path, type: which perl


# this script will take the standard output from probA and convert each 
# suboptimal alignment into a file that can be read by MODELLER

# this program was written by stewart pomerantz and adam c marko
# last modification was 1.13.2006

# questions please contact marko@psc.edu

##############################################
#		PROBA2PIR v0.1
##############################################

# To run this:
# type: proba2pir.pl -if <filename> -of <outfilename> -structure u/l 
#                     -first <value> -last <value>

# -if <filename> refers to the proba output file, you must capture it with 'script' or copy paste
# -of <outfilename> refers to the name you wish to have on the ali files
# -structure = which seqeuence id either upper (u) or lower (l) 
#              is associated with a structure (template)
# -first = first residue of protein structure (template)
# -last  = last residue of protein structure (template)
#
# Running this script successfully should result in
# an .ali file for each suboptimal alignment
#

# usage statement
$nargs = scalar(@ARGV) ;
#this checks the number of arguments/gives usage                                                                       
if( $nargs != 10 ) {
        print("usage: proba2pir.pl -if <filename> -of <outfilename>\n") ;
        print("       -structure <u|l> -first <value> -last <value>\n") ;
        exit(1) ;
}
 
for( $i = 0 ; $i < 10 ; $i++ ) {
 
        if( $ARGV[$i] eq "-if" ) {
                $inputfile = $ARGV[$i+1] ;
                next ;
        }
 
        if( $ARGV[$i] eq "-of" ) {
                $outputfile = $ARGV[$i+1] ;
                next ;
        }
 
        if( $ARGV[$i] eq "-structure" ) {
                $structure_id = $ARGV[$i+1] ;
                next ;
        }
 
        if( $ARGV[$i] eq "-first" ) {
                $first_res = $ARGV[$i+1] ;
                next ;
        }
 
        if( $ARGV[$i] eq "-last" ) {
                $last_res = $ARGV[$i+1] ;
                next ;
        }
}
 
print("==== input ====\n") ;
print("input file:   '$inputfile'\n") ;
print("output file:  '$outputfile'\n") ;
print("structure id: '$structure_id'\n") ;
print("first res:    '$first_res'\n") ;
print("last res:     '$last_res'\n") ;
print("===============\n") ;
 
 
open(FILE,"<".$inputfile) || die "Error: Could not open file '$inputfile'. Exiting.\n"
;
@lines = <FILE> ;
close(FILE) ;
 
$nlines = scalar(@lines) ;
 
 
##
## capture the sequence info
##
# $sequence_no = 0 is uppper sequence
# $sequence_no = 1 is lower sequence
#
  
$start = 0 ;
$middle = 0 ;
for($i = 0, $sequence_no = -1 ; $i < $nlines ; $i++ ) {
 
        if( $lines[$i] =~ /# > (\w*)/ ) {
                $sequence_no++ ;
                $sequence_name[$sequence_no] = $1 ;
 
                $start = 1 ;
                next ;
        }
 
        if( $start == 1 ) {
                $sequence[$sequence_no] = $sequence[$sequence_no] . $lines[$i] ;
                $start = 0 ;
                $middle = 1 ;
                next ;
        }
 
        if( $middle == 1 ) {
                if( $lines[$i] =~ /#/ ) {
                        $middle = 0 ;
 
                        if( $sequence_no == 1 ) {
                                last ;
                        }
 
                        next ;
                 }
                  
                $sequence[$sequence_no] = $sequence[$sequence_no] . $lines[$i] ;
        }
 
}
 
printf("name: '$sequence_name[0]'\n") ;
$sequence[0] =~ s/# // ;
$sequence[0] =~ s/\n//g ;
printf("seq:  '$sequence[0]'\n") ;
 
printf("name: '$sequence_name[1]'\n") ;
$sequence[1] =~ s/# // ;
$sequence[1] =~ s/\n//g ;
printf("seq:  '$sequence[1]'\n") ;
 
##
## capture the alignment info
##
 
$nextline = $i ;
$foundstart = 0 ;
for($i = $nextline, $alignment_no = -1 ; $i < $nlines ; $i++ ) {
 
        if( ($lines[$i] =~ /[\|\:\.\^]/) && ($foundstart == 0) ) {
                $alignment_no++ ;
                $alignment[$alignment_no] = $lines[$i] ;
 
                $foundstart = 1 ;
        }
 
        if( ($lines[$i] =~ /\d/) && ($foundstart == 1) ) {
                
				$foundstart = 0 ;
        }
 
        if( $alignment_no > -1 ) {
                $alignment[$alignment_no] = $alignment[$alignment_no] . $lines[$i] ;
        }
}
 
for( $i = 0 ; $i <= $alignment_no ; $i++ ) {
        $alignment[$i] =~ s/\n//g ;
        @result        = split(' ',$alignment[$i]) ;
        $alignment[$i] = $result[0] ;
       # print("alignment $i: $alignment[$i]\n") ;
}
 
##
## the alignment phase
##
 
 
for( $i = 0 ; $i <= $alignment_no ; $i++ ) {
 
        $ot_seq[0] = "" ;
        $ot_seq[1] = "" ;
         
        $idx0 = 0 ;
        $idx1 = 0 ;
 
        #print("translation for alignment $i:\n") ;
        #this translates the output to an alignment
		
        for( $j = 0 ; $j < length($alignment[$i]) ; $j++ ) {
                                                                                       
                $char = substr($alignment[$i],$j,1) ;
 
 
                ### fill in code here
                 
                if( ($char eq '|') || ($char eq ':') ) {
                 
                        $letter = substr($sequence[0],$idx0,1) ;
                        $ot_seq[0] = $ot_seq[0] . $letter ;
                        $idx0++ ;
                         
                        $letter = substr($sequence[1],$idx1,1) ;
                        $ot_seq[1] = $ot_seq[1] . $letter ;
                        $idx1++ ;
                }
                 
                if( $char eq '.' ) {
 
                        $letter = substr($sequence[0],$idx0,1) ;
                        $ot_seq[0] = $ot_seq[0] . $letter ;
                        $idx0++ ;
                 
                        $ot_seq[1] = $ot_seq[1] . "-" ;
                 
                }
 
                if( $char eq '^' ) {
 
                        $ot_seq[0] = $ot_seq[0] . "-" ;
                 
                        $letter = substr($sequence[1],$idx1,1) ;
                        $ot_seq[1] = $ot_seq[1] . $letter ;
                        $idx1++ ;
                }
 
        }
 
       # print("$ot_seq[0]\n") ;
       # print("$ot_seq[1]\n") ;
         
        #
        # output to the file
        #
	    
 #This will normalize the names so that the numbers all have 6 characters
		$normal=0;
		$namelength=length($i);
	    until ($namelength == 6) 
		{
		 $i = $normal . $i;
		 $namelength=length($i);
	    }

        $filename = "$outputfile" . "_$i.ali" ;
		 
        open(FILE,">".$filename) || die "could not open file '$filename'. Exiting. " ;
 
        # sequence 0
 
        if ( $structure_id eq "u" ) {
 
                print FILE (">P1; $sequence_name[0]\n") ;
 
        } else {
                print FILE (">P1; $sequence_name[0]_$i\n") ;
        }
 
        if( $structure_id eq "u" ) {
                $test = "structure:$sequence_name[0]:" ;
                $test = $test . "$first_res" ;
                $test = $test . ":A:" ;
                $test = $test . "$last_res" ;
                $test = $test . ":A::::" ;
                 
 
                print FILE ("$test\n") ;
 
        } else {
                $test2 = "sequence:$sequence_name[0]_$i" ;
                $test2 = $test2 . "::::::::";
 
                print FILE ("$test2\n")
 
                #print FILE ("sequence:$sequence_name[0]_$i\n") ;
        }
 
        print FILE ("$ot_seq[0]*\n") ;
 
        # sequence 1
         
        if ( $structure_id eq "l" ) {
 
                print FILE (">P1; $sequence_name[1]\n") ;
 
        } else {
 
 
                print FILE (">P1; $sequence_name[1]_$i\n") ;
        }
 
        if( $structure_id eq "l" ) {
                $test = "structure:$sequence_name[1]:" ;
                $test = $test . "$first_res" ;
                $test = $test . ":A:" ;
                $test = $test . "$last_res" ;
                $test = $test . ":A::::" ;
                 
 
                print FILE ("$test\n") ;
         
        } else {
                $test2 = "sequence:$sequence_name[1]_$i" ;
                $test2 = $test2 . "::::::::";
 
                print FILE ("$test2\n")
 
        }
 
        print FILE ("$ot_seq[1]*\n") ;
 
        close(FILE) ;
         
        print("wrote $filename\n") ;  # tells us that the files have been written
}