--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/bacteriaRegulatoryRegion_Detection/splitTranscriptGff.pl	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,189 @@
+#!/usr/bin/perl -w
+###
+# Main : defining utr and intergenic operonic intervalles from a transcripts file following a referencies file 
+# 
+# Input : 2 gff files to intersect, transcript queries vs referencies
+#
+# Output : resulting gff file printing to standard output
+#
+###------------------------------------------------------
+use vars qw($USAGE);                      
+use strict;                               
+
+=head1 NAME
+
+splitTranscriptGff.pl - compare 2 input gff files and define utr and intergenic operonic intervalles by couple of overlapping elements
+
+=head1 SYNOPSIS
+
+% intervallsExtractorGff.pl -i referencies.gff -j transcriptQueries.gff -s strand [-h] 
+
+=head1 DESCRIPTION
+This script will intersect 2 gff files and compute distance between 2 successives lines. Take care both of sorting by positions the input files and of that referencies are included in transcriptQueries.
+
+    -i|--input1 fileName   gff input file name: included elements
+    -j|--input2 fileName   gff input file name: extended elements
+   [-s|--strand] [s|d]	   s for single strand (colinear) or d for double strands (antisense) [default d]
+   [-h|--help]             help mode then die                              
+
+=head1 USECASE
+Define many fragments for each extended element (transcript): UTR5, gene, UTR3, "inOperon" for intergenomic region between 2 genes
+intervallsExtractorGff.pl -i CDSannotations.gff -j RNAseqTranscripts.gff  > UTRsGenesOperonsLists.gff;
+
+=head1 KWON BUGS
+No disjonction of overlapping elements of the included elements (-i file).
+In usecase, overlapping genes are fused in one long gene.
+
+=head1 AUTHOR
+Claire Toffano-Nioche - sep.11
+
+=cut
+#-----------------------
+sub feedPositionTab { my ($val, $pF, $pB, @info) = @_ ;
+		#print "feedPositionTab::$#info, ", ($#info+1)/4," \n";
+	for (my $i=0 ; $i <= $#info ; $i+=4) { # for each extended element 
+			#print "....$info[$i+2]\n";
+		if ($info[$i+3] =~ /\+/) {
+			for (my $c = $info[$i+1] ; $c <= $info[$i+2] ; $c++) { @$pF[$c]=$val } ; # sequence Forward
+		} else {
+			for (my $c = $info[$i+1] ; $c <= $info[$i+2] ; $c++) { @$pB[$c]=$val } ; # sequence Backward
+		}
+	}
+		#print "feedPos...:: ", join(".", @$pF[0..100]), "\n";
+		#print "feedPos...:: ", join(".", @$pB[0..100]), "\n";
+}
+#-----------------------
+sub recupInfo {	my ($pInfo, @lines) = @_ ;
+    for (my $i=0 ; $i <= ($#lines+1)*4-1 ; $i+=4) {
+    	my @line = split("\t",$lines[$i/4]);
+		push(@$pInfo, $line[0], $line[3], $line[4], $line[6]) ; # 0=nom, 3=debut, 4=fin, 6=sens
+	}
+	#print "recupInfo::fin=", ($#lines+1)*4, "\n" ;
+}
+#-----------------------
+sub tagName { my ($seqN, $posB, $posE, $strand) = @_ ;    
+	my $tagN=$seqN.$strand.$posB."..".$posE;
+		#print "tagName:",join("_",@_)," et tagName:$tagN\n";
+return $tagN;
+}
+#-----------------------
+sub transitionAnalysis {
+my ($pos, $seq, $s, $pdebAmont, $pfinAmont, $pdebIn, $pfinIn, $pdebAval, $pfinAval, $ptag) = @_ ;
+	my $enCours = 0 ; my $precedant = 0 ;
+	$enCours = @$ptag[$pos] ; 
+	$precedant = ($s =~ /\+/?@$ptag[$pos-1]:@$ptag[$pos+1]) ; 
+    if ($enCours ne $precedant) {
+    	#print "transi...:: $s, $pos, $precedant, $enCours\n";
+    	#print "transition::$$pdebAmont, $$pfinAmont, $$pdebIn, $$pfinIn, $$pdebAval, $$pfinAval\n";
+    	SWITCH: for ($precedant.$enCours) {
+               	/01/ && do { $$pdebAmont = $pos ; last SWITCH ;};
+                /02/ && do { $$pdebIn = $pos ; last SWITCH ;};
+                /10/ && do { $$pfinAval = ($s =~/\+/?$pos-1:$pos+1) ; 
+                		if (($s =~ /\+/)and ($$pdebAval!=$$pfinAval)) {
+                			printf "%s\tsplit\tutr3\t%s\t%s\t.\t%s\t.\tName=%s;\n", 
+                				$seq, $$pdebAval, $$pfinAval, $s, &tagName($seq, $$pdebAval, $$pfinAval, $s) ; 
+                			#if ($$pdebAval==$$pfinAval) { print "transition 10 +\n"};
+                		} elsif ($$pfinAval!=$$pdebAval) {
+                			printf "%s\tsplit\tutr3\t%s\t%s\t.\t%s\t.\tName=%s;\n", 
+                				$seq, $$pfinAval, $$pdebAval, $s, &tagName($seq, $$pfinAval, $$pdebAval, $s) ; 
+                			#if ($$pfinAval==$$pdebAval){ print "transition 10 -\n"};
+                		}
+                		$$pdebAval = 0 ; $$pfinAval = 0 ;
+                		last SWITCH ;
+                	 };
+                /12/ && do { $$pdebIn = $pos ; $$pfinAmont=($s =~/\+/?$pos-1:$pos+1) ;
+                		my $type="utr5";
+                		if ($$pdebAmont == 0) { # in case of interOperon : utr5-CDS-interOperon-CDS-utr3
+                			$$pdebAmont=($s =~/\+/?$$pfinIn+1:$$pfinIn-1) ; 
+                			$type="inOperon" ;
+                		}
+                		if (($s =~ /\+/) and ($$pdebAmont!=$$pfinAmont)) {
+                			printf "%s\tsplit\t%s\t%s\t%s\t.\t%s\t.\tName=%s;\n", 
+                				$seq, $type, $$pdebAmont, $$pfinAmont, $s, &tagName($seq, $$pdebAmont, $$pfinAmont, $s) ; 
+                			# if ($$pdebAmont==$$pfinAmont) { print "transition 12 +\n"};
+                		} elsif ($$pfinAmont!=$$pdebAmont) {
+	                		printf "%s\tsplit\t%s\t%s\t%s\t.\t%s\t.\tName=%s;\n", 
+                				$seq, $type, $$pfinAmont, $$pdebAmont, $s, &tagName($seq, $$pfinAmont, $$pdebAmont, $s) ; 
+                			#if ($$pfinAmont==$$pdebAmont) { print "transition 12 -\n"} ;
+                		}
+                		$$pdebAmont = 0 ; $$pfinAmont = 0 ;
+                		last SWITCH ;
+                	 };
+                /20/ && do { $$pfinIn=($s =~/\+/?$pos-1:$pos+1) ; 
+                        if (($s =~ /\+/) and ($$pdebIn!=$$pfinIn)) {
+                        	printf "%s\tsplit\tgene\t%s\t%s\t.\t%s\t.\tName=%s;\n", 
+                				$seq, $$pdebIn, $$pfinIn, $s, &tagName($seq, $$pdebIn, $$pfinIn, $s) ; 
+                		} elsif ($$pfinIn!=$$pdebIn) {
+                		    printf "%s\tsplit\tgene\t%s\t%s\t.\t%s\t.\tName=%s;\n", 
+                				$seq, $$pfinIn, $$pdebIn, $s, &tagName($seq, $$pfinIn, $$pdebIn, $s) ; 
+                		}
+                		$$pdebIn = 0 ; $$pfinIn = 0 ;
+                		last SWITCH ;
+                	 };
+                /21/ && do { $$pdebAval=$pos ; $$pfinIn=($s =~/\+/?$pos-1:$pos+1) ; 
+                        if (($s =~ /\+/) and ($$pdebIn!=$$pfinIn)) {
+                        	printf "%s\tsplit\tgene\t%s\t%s\t.\t%s\t.\tName=%s;\n", 
+                				$seq, $$pdebIn, $$pfinIn, $s, &tagName($seq, $$pdebIn, $$pfinIn, $s) ; 
+                		} elsif ($$pfinIn!=$$pdebIn) {
+                			printf "%s\tsplit\tgene\t%s\t%s\t.\t%s\t.\tName=%s;\n", 
+                				$seq, $$pfinIn, $$pdebIn, $s, &tagName($seq, $$pfinIn, $$pdebIn, $s) ; 
+                		}
+                		#$$pdebIn = 0 ; $$pfinIn = 0 ;
+                		last SWITCH ;
+                	 };
+          }
+    }
+ }
+#-----------------------	
+my ($fileNameI, $fileNameE, $strand) = ("", "", 0) ;
+# command line check
+foreach my $num (0 .. $#ARGV) {
+        SWITCH: for ($ARGV[$num]) {
+        /--input1|-i/ && do { 
+			$fileNameI=$ARGV[$num+1]; 
+			open ( fichierGffI, "< $fileNameI" ) or die "Can't open gff file: \"$fileNameI\"\n" ; 
+			last };
+	/--input2|-j/ && do { 
+			$fileNameE=$ARGV[$num+1]; 
+			open ( fichierGffE, "< $fileNameE" ) or die "Can't open gff file: \"$fileNameE\"\n" ; 
+			last };
+        /--strand|-s/ && do { 
+			if ($ARGV[$num+1] eq "s") { $strand=1}; 
+			last };
+        /--help|-h/ && do { exec("pod2text $0\n") ; die };
+        }
+}
+# memory declarations:
+my @infoI ; my @infoE ;
+my $seqName ;
+my @tagF ; my @tagB ; # Forward and Backward sequence
+# data retrieval:
+my @linesI = <fichierGffI> ; my @linesE = <fichierGffE> ;
+close fichierGffI ; close fichierGffE ;
+		#print "gff files read ; number of lines : $#lines1 + $#lines2\n";
+		# positions management
+&recupInfo(\@infoI, @linesI) ;
+&recupInfo(\@infoE, @linesE) ;
+# treatement: 
+# transform gff lines into chromosomal position tags : 0 for nothing, 1 resp. 2 for extended resp. included elements
+if (($#infoI) and ($#infoE)) { 
+	$seqName=$infoI[0] ;
+		#print "fin : $infoE[$#infoE-1]\n";
+	for (my $i=0 ; $i <= $infoE[$#infoE-1] ; $i++) { $tagF[$i] = 0 ; $tagB[$i] = 0 ; } ; # "O" tag in all chr. positions
+		#print "seqName : $seqName\n" ;
+	&feedPositionTab(1, \@tagF, \@tagB, @infoE) ; # "1" tag for all extended elements
+	&feedPositionTab(2, \@tagF, \@tagB, @infoI) ; # "2" tag for all included elements
+		#print join("", @tagF), "\n";
+		#print join("", @tagB), "\n";
+	# transition management:
+	my ($beginUpstream, $endUpstream, $beginIncluded, $endIncluded, $beginDownstream, $endDownstream) 
+		= (0, 0, 0, 0, 0, 0) ;
+	for (my $i=1 ; $i <= $#tagF-1 ; $i+=1) {
+		&transitionAnalysis($i, $seqName, "+", \$beginUpstream, \$endUpstream, \$beginIncluded, \$endIncluded, \$beginDownstream, \$endDownstream, \@tagF) ;
+	}
+	($beginUpstream, $endUpstream, $beginIncluded, $endIncluded, $beginDownstream, $endDownstream) = ($infoE[$#infoE-1], $infoE[$#infoE-1], $infoE[$#infoE-1], $infoE[$#infoE-1], $infoE[$#infoE-1], $infoE[$#infoE-1]) ;
+	for (my $i=$#tagB-1 ; $i >= 1 ; $i-=1) {
+		&transitionAnalysis($i, $seqName, "-", \$beginUpstream, \$endUpstream, \$beginIncluded, \$endIncluded, \$beginDownstream, \$endDownstream, \@tagB) ;
+	}
+}
+exit(0) ;